ARCO-UserManual
Contents
1. 15 00 1300 2500 2 48 775 16458 o B E N perried 53 13 17 00 1700 200 pis 228 1520 D 6 IEEE E CO A CORN T ONT NN T NN NT NN RN Economie al el ABCD D Civilstage perra 70 83 17 00 17 00 24 00 1 54 9 185 14 0 EconomicalleveKABCD 0 Postalcode 20001 76 47 13 00 ho no ps ps ps D op Postalcode 29001 Civist Economical leve 7647 1300 i300 Jizoo i9 so B300 D Pestacade 25001 Econo fovistage mamed B125 1300 1800 hem he so bu Civistage single Economical leve 50 00 5 00 25 0 5000 114 00 1200 0 cmomiemGEr c owmesrge B62 2500 2500 Mm has 3m emp B PostalCode 29001 Civilst Economical level 66 67 10 00 10 00 1500 152 3 40 16800 0 14 SS SS SEL ONE UNES ONEMI NES oo BO NN NUDO ON si O w ppesticions Notes Do o P Ep ber ue champagne wineHghQ e e t t LAN AAA 44 gt OH H H He p e eo dh dh e LAS LA PISO 9 e eo s a 190199590909995 o0 Al C O a Bitlab software Association Rules collaborative tool Integrated suite for association rule discovering in medical and molecular data Annexes Version vl 8 November 2007 On line updated information available at http chirimoyo ac uma es arco Comments to ots ac uma es ARco Manuals and Tutorials Annexe 1 Data transformation tools Before producing transactions2. Ex264 ex273 ex285 ex270 ex279 ex272 Ex267 ex286 ex280 ex283 ex276 ex284 ex279 Ex268 ex270 Ex266 ex283 ex286 Ex266 Ex268 Ex268 ex271 Ex266 ex270 ex270 ex271 Ex266 ex271 Ex266 Ex268 ex271 4 4 70 po SS 10 50S Ao nO OSS yS 40 31 00 2 1 70 1 7 00 J J 10 AO zum OO 70 80 so 1 E 20 50 SSS 60 yO SD SSS 50 00 NOS ASA GSO OS HN NON F9 I9 t mo Go sjaol gt ll ee imi mi m rl rl rl al ll al rl rl ll rl al ll al rl Ll Ll La Lean y a o Rules Visualization tab Tab used to display rules Rules can be ordered by any of their numeric columns Antecedent Consecuent Confidence Support ABS Support Coverage Improvem Leverage Conviction Entropy RuleID 181 155 78 16 9 60 68 00 12 29 1 79 186 Jese 5610 75 6900 153 122 177 170 186 8824 271 ooo 44 2 459 82 ri Li86 7356 os eo 1229 Neo ao 176 fis 5294 508 Beo 960 121 os 176 rss 6290 S51 3900 876 293 js 211 69 196 i7 Liss oco 508 peoo 5 s 06 p pis t155 176 196 Bonn 508 jesoo 635 3306 G4 bes D v o 176 L186 7258 636 kso 876 ss hba hor Do po 19 Lis 8973 2345 16600 pois io 20 bass Do por tass Jese ass 2345 iso ja 12001 hss 0 o 186 ze ass rito 5 79 Wo 6336 301 fe D 155 176 186 9111 579 L00 amp 636 2 87 posse 0 0 0 1 J 1 J J J J J J J
3. ACETYLORNITINE_DEACETYLASE Hierarchical Items are often organised in hierarchical way and some transformations also produce hierarchical data This characteristic has effect in the expected support of item items at the lower level are expected to have lower support Since some fields of the transactions database have this structure ARco provides a way to re code the level at which the metadata are annotated Uniform support Flexible support Level 1 Vi Level 1 min sup 5 support 10 min_sup 5 Level 2 2 Milk Skim Milk i Level 2 min sup 5 support 6 support 4 min sup 3 Distance based data transformations Interval Equi Depth amp equi width Binning methods do not always capture semantic of data intervals In these situations a distance based partitioning can be used this is to say numeric attributes can be dynamically discretised to maximise the confidence or compactness of the rules This discretization can be done by accounting the number of points in a given interval or by closeness of points in an interval distance function Triming Keep the first or last n characters and it is available for all data types all datatypes are taken as string data ID ACETATE_KINASE ACETOIN DEHYDROGENASE ACETOIN DEHYDROGENASE ACETOIN DEHYDROGENASE ACETOIN DEHYDROGENASE El COMPONENTITPP DEPENDENT ALPHA SUBUNIT ACETOIN DEHYDROGENASE El COMPONENTITPP DEPENDENT BETA SUBUNIT ACET
4. 76 47 1300 1300 hzo 239 pse esmo QD S9 PostalCode Z Economicalle 76 77 13 00 1300 fiz 19 as bao Do o 1 o Postacode 2 Cistagema 81 26 i300 1300 600 L77 be eso Do M Civistage sin Economicalle E00 500 500 000 us 30 i20 Q0 1 2 LEcononical le Civistage sin 56 82 2500 ps0 400 quis Boo uso Q0 3 o PostalCode 2 Economical le 66 67 oco 10 00 i500 hse B o 680 Q0 4 Postando E A A E MN NEC NEN NNNM NNNM champagne Eu A NENNT E O E RENE PostalCode m champagne 100 00 8200 3200 200 oo 408 mn Do 3 o o bee esaCodep E400 ieo 600 O 256 575 208535 o qe o CN ree jeto CTC lie os 0088 bis mesi be Economical le PostalCode p 60 00 500 i00 ps 45 heo Do po EE ECEN Economicalle 62 50 1500 500 40 42 ha jos D o Porat mes 85s eo Ima Eri 15 0 heso Do pr PostalCode Zell wine High Q 10000 32 00 133 Bo infinity po 23 Economical le cvistagema Sea 1 00 2100 114134 113 40 o y A PP PS E A E E gt E E gt M M gt E M gt M TE all Filters lt lt O 306 gt gt Filtering by datatype E Experiments M Metadata Experiment Rules Antecedent and Metadata Rules Antecedent and Consequent are expresi n values Consequent are metadata values E gt E E gt M M gt E M gt M Show all Filters t t Experiment M
5. Used to save files transactions frequent itemsets or rules depending on the tab Expand Expand button Displays the advanced options in the transactions generation tab Proceed Proceed button Launch the corresponding process Next Previous buttons browse and surfing the multiple pages tables ARco organization Tabs ARco is organised in four main modules the natural steps in association rule discovering procedures l 2 3s 4 Data manipulation to produce a set of transactions to be mined Finding frequent itemsets in the transactions file Produce association rules Browsing and exploring results Following these steps the Control Pane has the next tabs or sub sections Transactions Frequent Item Sets Rules Data view filtering transforming and coding tools to produce transactions Algorithms to produce Frequent Item Sets k itemsets set of k items frequently present together in the same transaction Parameters for association rules production Visualization filtering translation and exploring rules Other secondary tabs HeatMap Histogram Original Data View Visualization Panel Info Tabs ARco Heatmap representation of expresi n data Histogram representation of expresi n data Displays the original Transactions that holds the a selected rule Rule profile display Different informative tabs associated with a given action Manuals and Tutorials From original data to Tran
6. hh l d A AAA ne b t PS t ht st og dose does a Bitlab software Association Rules collaborative tool Integrated suite for association rule discovering in medical and molecular data User Manual Version vl 8 November 2007 On line updated information available at http chirimoyo ac uma es arco Developed by Jes s Jim nez Espada Javier Rios Andr s Rodr guez Oswaldo Trelles Report incidences to ots a ac uma es ARco Manuals and Tutorials ARco pipeline As described in the Introduction section Arco has been organised to fulfil the KDD procedure integrating a diverse gallery of methods with different but combined scope At the end or as one important part of KDD we devise ARco that should take place in the data selection transforming processing and high level analysis including visualization for human analysis of the new expressed knowledge in the form of association rules or the co occurrence of events from which is possible to produce a conclusion with certain degree of confidence Next picture depict a sketch of this chain as we see it Selection Ea Rules Transforming shk Frequent Production and coding sp ms K itemsets Sketch of the chain of association rule discovering using Arco First step in this chain is the selection of the data relevant to be subject of analysis Over this selected dataset is necessary in general operate on it to focus
7. it is possible to perform some data transformations with the aim to increase the probability of discovering new knowledge For instance if we have extremely descriptive metadata e g patient age it will be difficult to incorporate this metadata in a frequent itemset Therefore it could be better to define some categories or groups with similar metadata e g age ranges 0 10 11 20 21 40 41 60 61 85 86 After rule generation to allow a better analysis the original data are shown in the Original Data View tab The following transformations are available for metadata Trimming Kept the first T characters Protein Annotations AS Example Trimming the 20 first CE o Trimming reduce the metadata space characters will code the boxes ACETOIN_DEHYDROGENASE TAM e de ACETOIN DEHYDROGENASE RS ie metadatas into the general ACETOIN DEHYDROGENASE E1 COMPONENT TPP DEPENDENT ALPHA SUBUNIT ACETOIN DEHYDROGENAS ACETOIN_DEHYDROGENASE_E1_COMPONENT TPP_DEPENDENT_BETA_SUBUNIT ACETOIN_DEHYDROGENASE_E2_COMPONENT DIHYDROLIPOAMIDE_ACETYLTRANSFERASE ACETOIN DEHYDROGENASE E3 COMPONENTIDIHYDROLIPOAMIDE DEHYDROGENASE A U A YNIH WAYURUAY AbUllioYINIHA AR JBU ACETOLACTATE_SYNTHASE_ ACETOHYDROXY_ACIDSYNTHASE _ SMALL_SUBUNIT ACETYL_COA_ACETYLTRANSFERASE ACETYL_COA_CARBOXYLASE_ ALPHA_SUBUNIT ACETYL_COA_CARBOXYLASE_SUBUNIT_ BIOTIN_CARBOXYLCARRIER ACETYL_COA_CARBOXYLASE_SUBUNIT_ BIOTINCARBOXYLASE_SUBUNIT ACETYL_COA_SYNTHETASE
8. Abrir con Java TM Web Start Launcher predeterminada v Advertencia Seguridad utom ticamente para los archivas como ste de ahora en adelante La firma digital de la aplicaci n no se puede verificar Desea ejecutar la aplicaci n Nombre Association Rules Program Editor Max Garcia De http imango ac uma es ARERR EERE P R PE PRE PERSE PRE aaa REPER REPER PRER RERE ane nana ERE RE RRAS REP S rrer nana nana aerea mae a ESE EH HH P R REE PES PP EP PARE GE REPER SP PE PRER PESE EP P RE PSE EE PERES AAA ARAS Ejecutar Cancelar confianza Ejecute esta aplicaci n solamente si conf a en el M s informaci n desarrollador QU La firma digital no se puede verificar mediante una fuente de Note Since ARco manuscript is in the evaluation process the software is only available upon request ARco main screen ARCO is organised in five frames each one with the ability to contain several sub tabs pannel Control tr Altra LE A Tiran Frapett kore Sets gt Rules ys we Extraccer Made 22 Fal Tirechoki eho wa E a Was Looe Treestad p sd n yu i on E pu Processing fer T A n use spend peje P i i TUER pos 3 information 0 E x Buh ase P im 4 s na p e t Dome e pos q ke E da rio Metadata r o pa pes a set t2 A lt E qem Y penart 1 AD AL AT AD vectors 100 rwn va JO IMA sers iD
9. Sun Developer Network SDN searchtips searct java APIS Downloads Technologies Products Support Training Sun com Developers Home gt Products amp Technologies gt Java Technology gt Java SE Download Java SE Downloads It s time Download the complete environment and runtime environment Get the JDK download o Java SE Site Map Regional Downloads Overview Technologies Reference Community Support dis Latest Release Next Release Early Access Previous Releases Japanese H t Confused or having trouble downloading or installing See the download help page Supported System Configurations G y Java JDK 6 Update 2 The Java SE Development Kit JDK includes the Java Runtime Envir and command line development tools that are useful for developing applets and Download Related Resources applications Compatibility Performance More info about Java SE 6 Update 2 E Security Mobility Installation Instructions ReadMe ReleaseNotes Sun License Third Party Licenses Related Downloads ML and Web Services ARco Manuals and Tutorials Download ARco from http chirimoyo ac uma es arco http chirimoyo ac uma es arco mango ac uma es ACGT jaws apps test Arco inl Abriendo Arco jnlp Ha escogido abrir La Arco jnip el cual es un JNLP File de http mango ac uma es Qu deber a hacer Firefox con este archivo
10. ety vakte 262 le reage SIN Zaro Ves ODOR Pastre ver SOSTE Pdsgatove Yer XN Feng ade tfang ong These restos pra presna Treeestad n ee sesion Teseshoat 0 0 e pressa vhs 257 Eri exyeeccend mos 1 Me sia e Customer i 100 100 gt 1 Pee ode 100 po corre X le 100 44 re Metadata information Mt old Olferert ele Mas Praga Hesio riia Heatmap images w wi Fin rescue Creme agn Fre Poe qd ban Tave t agp Support Cohen as A nm i1 LO Pashe 6 3 Sett mio gt 2 5 SS Batt Pes Beet The most important is the Control Pane in which the main ARco options are available and parameters are settled The Data frame contains original and processed datasets i e gene expression matrix or association rules Below the control pane one frame is devoted to display summarised information about data processing and also have a tab for graphical displaying of rules Heatmap frame contains different data representations and on the bottom specific information about selected data sets are provided Frame re sizing is available ARco Manuals and Tutorials Icons glossary Common elements are used in AR co with the same behaviour in different contexts Load button Used to upload a data file gene expression data in the Transaction tab a Transactions datafile in the Frequent itemset tab and frequent itemset datafile in the Rules Tab Browse Browse button
11. J J em e PQ ta 155 91 48 22 74 4 86 56 33 aL 138 176 E 5535 amp si G90 pe as O e 161 00 z0 fine 65959 ties 5194 om ra E09 15633 LS 7 4 5 Fi 1 4 4 123 00 i9 6477 feio i40 485 i9 ies rez 6i i40 pais i88 ins 6645 1427 hoo L4 196 j 188 5459 11427 hoioo PP E gt E E gt M M gt E M gt M Show all Filters lt lt D 134 IE TE I 188 155 80 92 17 37 95 79 220 16 J 6 187 6 J 1 37 2 1 56 oo S8 komn p th 0 0 s Clicking a given rule all transactions that hold the rule are highlighted in the Data frame Different filters are available E gt E E gt M M gt E M gt M Show all Filters Hide trivials Hide unproductive Custom Filter Experiment Experiment rules only expresi n values Experiment values antecedent implies a Metadata consequent Metadata in the antecedent and experiment value in the consequent Metadata Metadata rules Show all rules Advanced filters Remove trivial rules A rule is trivial if there 1s another rule with the same Right Hand Side and a subset of the Left Hand Side that covers exactly the same cases from the data set For example the first of the two rules below is trivial because it has the same coverage as the second Adding Tomatoes to the LHS of the second rule does not affect 1t Lettuce amp Tomatoes gt Cucumber Coverage 0 250 250 Suppo
12. OIN DEHYDROGENASE E2 COMPONENT DIHYDROLIPOAMIDE ACETYLTRANSFERASE ACETOIN DEHYDROGENASE E3 COMPONENT DIHYDROLIPOAMIDE DEHYDROGENASE ACETOLACTATE SYMTHASE ACETOHYDROXY ACIDSYNTHASE LARGE SUBUNIT ACETOLACTATE SYMTHASE ACETOHYDROXY ACIDSYNTHASE SMALL SUBUNIT In this example we can devise three main groups of annotations with at different level of detail One of the main purposes of data transformation is to increase the probability of a given itemset to be part of a frequent itemset However a disperse space of metadata can go on the converse direction This transformation allows to joint similar data under the same category increasing the support of the categories 5 Iriming Parameters X ACETATE KIMASE ACETOIN DEHYDROGENASE E ACETOIN DEHYDROGENASE ACETOIN_DEHYDROGENASE ACETOIN DEHYDROGENASE ACETOIN DEHYDROGENASE ACETOIN DEHYDROGENASE ACETOIN DEHYDROGENASE ACETOLACTATE SYNTHASE ACETOLACTATE SYNTHASE In the example the first 21 characters on the left are used to describe the category As result the descriptor keeps the main power but additionally several items will contain it Important note When a trimmed item is part of a rule ARco will display the original value of the item ARco Manuals and Tutorials Hierarchical This type of data transformation is used to reduce the deep level in a hierarchical metadata the metadata must be in the form of XsYsZ where X Y and Z are a category and s
13. e Improvement Minimal consecuent size Appearance Expand C tmp2 kobdat kob rul Confidence Minimum rule confidence rule reliability of X gt Y in T is the ratio of the of transactions in T containing X that also contain Y versus total of transactions in T containing X to produce a rule Improvement Minimum Improvement Minimal l How many items in the consequent side consecuent size By default any element can be at any place in the rule antecedent or consequent side Positional restrictions can be established for each item type to be in the antecedent in the consequent in both or not to be in the rule Hierarchical O Ant O Con Both O None Genes O Ant O Con Both O None x Ant Con Both O None y O Ant Con Both O None Ex263 O Ant O Con Both O None Ex264 O Ant O Con Both O None ex265 O Ant O Con Both O None Ex266 O Ant Con Both None Ex267 O Ant Con Both None Ex268 O Ant Con Both None Ant This data type can only be in the antecedent side of the rule Con This data type can only be in the consequent side of the rule Both This data type can be both in the antecedent or consequent side of the rule None Rules with this datatype are discarded Data View tab It becomes available when a data file has been loaded A table style is used to display the data set highlighting the cells involved in a transaction produc
14. etadata the Metadata gt Experiment the Shows all the rules antecedent is an expression antecedent is a metadata value and the consequent isa and the consequent is an metadata expression value Filtering by values 4 E gt E E gt M M gt E M gt M Show all Filters Hide Trivials i Custom filter e E Hide Unproductive Min Max Custom Filter Support Absolute O Coverage Improvement Leverage Conviction Output Filename C iguiaimarket 0 rul Set filtering parameters 1 ustom filter Sel Min Max 0 Support Absolute EN TEEN minimum parameter value Coverage Improvement Leverage Conviction Output Filename C iguiajmarket 0 rul EE HD E File pathname to store filtered rules ARco Manuals and Tutorials Visualization of transactions that hold the rule Antecedent Consecuent Confidence Support ABSSup Coverage Improve Lever Conviction or L RuleID ee seen D EG 29001 66 67 Postacade 25001 Economialevel 8000 heoo heoo 3200 208 Ba heo bo io Economical level ABCD C _ PostalCode pc29 51 36 27 00 27 00 4400 143 08 14753 pp e PostalCode pc29002 Econgggaplevel 62 79 27 00 27 00 800 43 g08 isos0 0 B Economical level ABCD 8 _ Postafifill pc29 61 90 15 00 1300 2100 2 48 775 19688 Q0 4 PostalCode pc29003 Econdiflfillevel 52 00
15. is a separator genName Functional category aceE Metabolism aceF pyruvate dehydrogenase E2 component ackA acetate kinase acpP carrier protein acpS holo acyl carrier protein synthase adk adenylate kinase ahpc hydroperoxide reductase C22 subunit thioredoxin like alaS alanyl ERMA synthetase amiB Peptidoglycan biosynthesis ans L asparaginase I apaH diadenosine tetraphosphatase apbE thiamine biosynthesis lipoprotein ApbE precursor FC level3 4 4 2 1 4 2 4 5 1 4 5 1 4 6 2 JJ LE Ju 4 4 2 4 6 2 4 8 11 In the example the functional category of genes is shown togeter with the geneName in the first row and the numeroc level of the category The deper the level is the more specific the description is Reduce specificity can be obtained by Hierarchical transformation vai Hierarchic Parameters Level Level Separator In this case we set a retdution to the second level those annotation whose original category is lower than 2 maintain their initial values Result of data transformation are displayed in the picture aceE Metabolism E ae pyruvate dehydrogenase E2 component 4 2 ack acetate kinase 4 2 app carrier protein 4 5 acp5 lhole acyl carier protein synthase 4 5 ak ladenylate kinase 4 6 ahpc Ihydroperoxide reductase C22 subunit thioredoxin like 13 3 alas lalany tRNA synthetase L2 amB PPeptidoglycan biosynthesis 5 2 ans IL asparaginasel 4 4 apaH Idiadenosine tetraphos
16. m values must be specified for each criterion Output is stored in a file ARco Min Max III LLI LLI ILIR LLLLLI ETT Support Relative Support Absolute Improvement 0 0 0 Coverage 0 0 Leverage 0 0 Conviction Output Filename Manuals and Tutorials Heat Map tab This frame 1s used to display a visual representation of gene expression values in the form of a coloured matrix Traditionally expression values have been represented using red for over expression and green for under expressed genes The colour scale also includes a black range for values log2 ratios close to zero and red and green scale for different values including a saturation point from which all the values receive the same colour Image can be saved to disk using right button Save image functionality The colour palette and saturation points are customisable Right button Colours Palette ror o MOBO vec E OB OO Over and under colours are used for over expressed and under expressed genes Changes affect Data view representation In the main body there are 4 vertical lines that can be horizontally moved to define the non differentially expressed range around log ratio equal cero and under over expressed points at which the signal become saturated al values at the left in the under expression side or all values on the right of the saturation points are coded with the same c
17. olour Histogram tab Histogram of gene expression values original data 2 6110700934579443 Numerical values are shown on the bottom bar when the mouse moves over the image Original Data View tab This frame is used to display the transactions that hold the rule selected rule and only will be availbale after the rule selection event G10081 1 2 3 2 3 95 paal 16 G10833 1 2 4 2 3 7 ybbC yzbB 83 G11571 1 2 3 2 3 8 bb 39 G12711 1 2 3 2 3 10 ybcL 56 311504 1 2 4 2 3 12 Esg 12 G10173 1 2 4 2 3 19 lycxB 30 G12053 1 2 3 2 3 21 ydaE 31 312067 1 2 3 2 3 22 ydaT 49 312804 1 2 3 2 3 30 ydjN 46 312841 1 2 3 2 3 33 WwerO 27 Visualization tab Hierarchical Genes X y Height Age Gender Exp cJ ES f pe 153 193 22 Female Ex264 0 165249 0844746 0 613583 274507 539159 0792633 184233 12063 461179 0 31034 167 I2 Female ex265 13 516 0 428843 0 415037 0 303781 0 0 0 053638 138 215 116 046 EESTI 0 304855 186 188 156 188 21 11 Female Male Ex266 Ex267 247438 223 704 119 265 196 963 147 089 124 691 0 406424 201634 0 464963 10 889 165 22 Male Ex268 107 039 112 873 0 89743 247 249 0 793549 0 527247 135 669 144 057 133 985 D 0687128 For E E rules displays the gene expression profile or the sample profile for transposed matrices with red lines and the experiments that hold the rule g
18. olute value number of transactions or relative percentage When working with multiple supports by item support this parameter must be specified for each different item Unique the same support for all items Multiple specific support for each item Minimal k value Maximum k value Available for Unique support Available for Unique support These options and parameters are needed to produce frequent k itemset with general support If individual supports are needed for each item we can use the button Min support Max support Support Type Relative lt Relative lt Relative lt Relative lt All the item labels are displayed and a dialog box can be used to set individual supports both modes and values A table with the following parameters is available Name Item label it can correspond to an item an item metadata or sample metadata Min support Minimum support for this item Max support Maximum support for this item Support Type Absolute number of transactions or relative as percentage All values can be modified at the same time using right button functionality Fir instance to set to Absolute all the Support type you can click right button over any cell in the Support type column the same is valid for support values ARco Manuals and Tutorials Rules Tab Option and parameter related with rule production Transactions Frequent Item Sets Rules Confidenc
19. phatase 4 6 apb thiamine biosynthesis lipoprotein ApbE precursor 4 8 genName Functional category FC level3 Data categorization These transformations allow to group numerical values into a reduced set of categories partitioning The next options are available Equi Depth interval transformation Each partition interval has the same number of items E Equi depth Parameters Ed Number ofintervals 4 In the example 4 groups have been Es created with similar number of Rs elements ol LDL 1 0 17 0 1 0 17 0 Each partition interval has the same size range and interval sizes are required ae Groups values between 3 and 60 in intervals of size 9 ARco Manuals and Tutorials Annexe 2 File formats engene 0 format dat htto chirimoyo ac uma es engenet An engene data file is a table This table is stored in the file as a set of fields separated by TAB and along several lines This text format may be worked out by Excel So an Excel table as follows will generate a file as shown below when it is saved as text 16 123 15 151 ES 37 916 Data are a collection of vectors one vector a row All vectors have the same number of variables one variable a column Some values may be unknown in this case the respective field may be a non numeric string o may be null These values are called NaN Not A Number In the picture these values are red marked It is
20. possible to append notes to data This kind of information is called metadata There are three types of metadata global labels row labels and column labels All labels have two parts the label_name and the label_values For each global labels name there is only one value Row labels have one value for each data row and column labels have one_value for each data column Next picture shows how to put labels to data ASA abels names 1 e blue Global d the values 1 16 72 etween 123 15 1 pace in next lave fields A SD INE and com CTagiName CTagivall CTaglVal2 CTagiwan Next figure ning after the Clag2Name ClagzVal1 Clag2val2 Clag2Wa in the figure sem alo fares klaqiName E xcel you must RTag vall 1 16 on used to RTag1val2 123 15 T RTad1 val 151 15 decimal separator common amp win Gene or row Metadata labels are shown in red and data in orange Dark green represents sample or experiment column metadata labels and light green column metadata values Gene expression ratios are shown in blue The same format is valid as xls Excel file or TSV text tabulated CVS comma separated files ARco Manuals and Tutorials m n Sian DE np BE a a EE SE aa DE oa ea Gene or row Metadata labels are shown in red and data in orange Dark green represents sample or experiment column metadata labels and light green column metadata values Gene expression ratios are shown in bl
21. reen boxes Options to modify the representation are available on right buttom Change View Show backgroundgrid Show all profiles Displays a grid OFF displays the gene expression profile of those genes holding the rule ON displays all the gene expression profiles as a background 1mage the gene expression profile of those genes holding the rule coloured in the foreground and the green boxes for items involved in the rule Draw lines Draw dots ARco Displays only the green boxes or also draws a rule profile joint with a line all the points Manuals and Tutorials Filtering rules Antecedent onsecuent Confidence Support ABS Support Coverage Improvement Leverage Conviction A zn Economical le Postalcode 2 66 67 16 00 16 00 24 00 2 08 8 32 204 00 A pen Economie E00 e 00 e000 jo iex fio 8 J Economicalle PostaKCodep 61 36 27 00 2700 400 fa Bbo 4553 Do P Powel pe Tecononesl 2 7570 or 00 300 Tue so 15050 Do OB Economicalle Postalode p 61 80 1300 13 00 100 es 5 hes Q0 8 PostalCode p Economical le 52 00 3 00 13 00 500 pas 75 h ss Do S PostalCode 2 Civistage ma 63 13 7 00 1700 200 us a so o b o Postalcodep Civistage sm 55 8 p400 400 4300 Li2 250 fuse Do 7 Economicalle Cwistage ma 70 88 7 00 17 00 p400 94 595 8 amp i4 Q0 8 Economicalle PostalCode 2
22. rt 0 239 239 Strength 0 956 Lift 2 91 Leverage 0 1568 156 Lettuce gt Cucumber Coverage 0 250 250 Support 0 239 239 Strength 0 956 Lift 2 91 Leverage 0 1568 156 If a rule is trivial then it will have the same support strength lift and leverage as the rule with respect to which it 1s trivial see http www rulequest com M Ofiltering html Unproductive rules A rule is unproductive if there is another rule with the same Right Hand Side and a subset of the Left Hand Side that has equal or higher strength For example the first of the rules below is unproductive because it has lower strength than the second Adding Promotion1 f to the LHS of the second rule decreases its performance Profitability99 lt 419 amp Promotion1 f gt Spend99 lt 2030 Coverage 0 274 274 Support 0 248 248 Strength 0 905 Lift 2 72 Leverage 0 1568 156 Profitability99 lt 419 gt Spend99 lt 2030 Coverage 0 333 333 Support 0 302 302 Strength 0 907 Lift 2 72 Leverage 0 1911 191 If a rule is unproductive then it will have the same or worse support strength lift and leverage as the rule with respect to which it 1s unproductive see http www rulequest com M Ofiltering html Customised filter Customised filters allow combining different requirements to filter the rules In the available dialog box several criterions can be used at the same time confidence support coverage etc and minimum and maximu
23. sactions This section contains the Control Pane with the working options and needed parameters It contains filtering parameters items selection and transformation metadata identifiers etc Transactions Frequent Item Sets Rules Extraction Mode O PYalues Threshold PYalue Upper Threshold Lower Threshold Replace items by metadata L C tmp2ikobdat kob tr P Parameters Extraction Mode pvalue Upper Threshold Lower Threshold Relpace items by metadata L Apply Transpose Data Used to transform expression values into 3 state elements over and under expressed and not differentially expressed Two methods are available Thresholds under and over and p values Maximum p value to set an expression value as differentially expressed required when using the p value extraction mode Under this option the pvalue associated to each expression ratio will be computed from the z scores normalised ratios with mean zero and standard deviation 1 Over expression threshold Minimum expression value to be set as over expressed required when using the threshold extraction mode Under expression threshold Maximum expression value to be set as under expressed required when using the threshold extraction mode Instead of including the item ID in a transaction it is replaced with the experiment metadata sample or column metadata Perform the data filtering using the extrac
24. the processes in particular features Data transformations reduction and compacting hierarchical simplification diverse alternative coding procedures etc are important procedures in this step A collection of transactions in the form of a list of numbers that represent events that co occur simultaneously is the resulting output This output is the input to identify k itemset set of k items appearing together more frequently than expected by chance From these frequent k itemsets it is possible infer rules with certain confidence estimated from the dataset Steps ARco is endowed with different algorithms to be applied on the same data set in pipeline fashion This guided tour will shown each of these procedures in the following order a Installation guide b Load Step which includes filtering and transforming data to produce a transaction dataset c Mining transactions to identify frequent k itemsets d Ruling the frequent k itemset to produce rules e Analysis procedures ARco installation guide Java support has been chosen vvith the aim to extend the scope of ARco Installing a Java virtual machine available for most of the current operating systems is enough to have a full operative environment System Requirements Java virtual machine 1 50 or latter gt Last version of ARco software Java virtual machine http java sun com javase downloads index is Java Solaris Communities My SDN Account Join SDN
25. tion Some data manipulation tools are available on right button functionality clicking over the column to be modified Data View XORF Hierar Genes x 10065 10066 310077 10078 em pure 24 2 dek yaaF 113 G10081 11 2 3 2 yal 16 G10100 1 2 4 2 G11565 G10837 11 2 4 2 feuC SIE 1 2 3 2 G10833 1 2 4 2 G10832 J1 2 3 2 G11566 1 2 4 2 G11567 1 2 3 2 G11569 G11571 G11572 G10166 G10167 G10949 1 2 3 2 ndhF ybxE TIT a k gi gi gi wo CO P9 em _ di pudo a v Triming Keeps the first or last n characters Hierarchic Reduce the deep level value in a hierarchical codification Interval Equi Depth Identify n different groups with equal number of elements equalization Valid for numerical data Interval Equi Width Produce n different groups with the same range size Require min and max values and interval size Undo Transformation Un do the last transformation Reload Column Un do all transformations performed on a given column re load original values Annexe lcontains detailed information for data transforming procedures ARco Manuals and Tutorials Frequent Items Sets Visualization tab Displays the frequent item sets It can be explored and ordered by the item support absolute or relative Frequent Item Sets Support Number of transactions 1 80 2 00 40 00 oS 10
26. tion mode and associated parameters and up dates the corresponding images Transpose the matrix row columns interchanging Obviously it includes metadata Generate transaction from filtered data Proceed Advanced options are displayed when click on expand button Column ID Row ID Row Metadata Hierarchical Experiment sample or column identifier Gene or row identifier Columns Ex263 Ex264 ex265 Ex266 Ex267 Ex268 Ex269 ex270 In the main body of the dialog box row and column metadata can be activate inactivate to participate in the mining procedure ARco Manuals and Tutorials Frequent Item Set tab Frequent k itemset production procedure is controlled from this tab Main parameter are Support number of transactions containing a given k itemset maximum k value and algorithm Algorithm Support Type Support Mode Minimal number ofitems Maximal number ofitems Minimal support Maximal support Transactions Frequent Item Sets Rules Algorithm Borglet Ard Support Type DSL Rejat Support Mode C Unique e Multiple Minimal number of items 1 Maximal number of items 5 Minimal support Maximal support Multiple supports w C tmp2 kobdat kob Fis Browse Two options are available Extended variable support Borgelt proposal http www borgelt net apriori html Rodriguez et al http www biomedcentral com 1471 2105 7 54 In abs
27. ue
Download Pdf Manuals
Related Search
ARCO UserManual arco manual arco manual handling