Download_data_from_aassession_number00 The name of the affymetrix experiment 2013-08-30 08:35:50.661 UTC E-GEOD-3790 2013-08-30 08:19:57.365 UTC directory00 The directory to download the data from the affymetrix database into. 2013-08-30 08:39:13.884 UTC array_number00 This input indicates which gene information to further process. 1 -> for gene expression from Array A 2 -> for gene expression from Array B 2013-08-30 09:26:32.202 UTC 1 2013-08-30 09:26:34.809 UTC download_datadatadirectory0arrayfile0 download data from ArrayExpress 2013-11-02 14:06:48.440 UTC net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity arrayfile 0 false datadirectory 0 false false localhost 6311 true false arrayfile STRING datadirectory STRING net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_expressionset_objectarray_number0 This part loads the files that were saved in the local directory previously. The expression file is tranformed in log2. The ExpressionSet is created and the two files, the expression and the phenotype file are exported and saved in the directory specified in the input port. 2013-10-31 16:02:55.766 UTC net.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivity array_number 0 false false localhost 6311 true false array_number DOUBLE net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokedownload_datadatadirectorydirectorydownload_dataarrayfileassession_numbercreate_expressionset_objectarray_numberarray_number 7d7b3cd3-cec9-4756-ba1e-f3e01ad6622e 2013-11-02 15:12:34.945 UTC cf3575ca-7679-4789-8356-e98551a3809e 2013-11-02 14:41:51.692 UTC 59a70cee-a42b-4a4e-859f-fcf78bd5bafe 2013-08-30 09:23:32.240 UTC 34579faa-f9e4-4caa-9404-b99dd954899b 2013-02-05 15:32:31.596 UTC 92111295-ef19-4b77-a4f3-c6eea49ebdee 2013-08-30 09:25:23.817 UTC 75cacdff-de0c-4a9f-8fad-36bdd4a7c0e1 2011-07-29 13:54:13.219 UTC 24de6446-4e4e-4682-9470-debea08551dc 2011-07-29 15:10:45.81 UTC 087d6cfb-c512-490b-874b-ad1dceaf36fb 2013-08-30 08:23:58.661 UTC 0fea4cef-1539-4116-9862-122a9886326a 2011-07-28 14:39:36.521 UTC 4a9df8c8-46dc-4651-b803-9cb9b75ba1a9 2013-08-30 08:39:15.84 UTC 390197ef-6ce5-45e4-b4f9-2bef9ec19da5 2011-07-28 14:12:18.670 UTC cfb3b64d-e1cd-4461-a881-6a0d04efa4de 2013-02-05 16:19:05.889 UTC 54807056-888f-449a-8b6e-67053f8b4d64 2013-08-30 08:21:15.216 UTC Download data from array express + create expressionset object 2013-08-30 08:21:15.116 UTC 792f6229-dea0-47de-a6f4-ee97fdd167d9 2013-08-27 12:13:01.404 UTC 85f1e353-34e7-4e75-96d6-3c9bc6034947 2011-07-29 13:47:09.796 UTC ca6d5881-decb-45f6-9d3f-ed3dd5f7a05e 2011-07-28 14:15:57.633 UTC 16bcc0c7-c4f6-4804-b1ea-14863d796ca8 2013-02-06 13:00:10.847 UTC a1ff243b-3e94-46c7-98c4-6c6fe977159f 2013-08-30 09:21:00.242 UTC 9b03d198-4c13-4853-9c12-3223e1d86412 2013-11-02 15:06:13.949 UTC 7ab1d0ff-6892-4dd1-aa74-b45b7fea89d3 2013-08-30 09:26:33.776 UTC f55fc447-2680-4150-a6e2-524cae0d4bcd 2013-02-05 15:32:12.230 UTC b117bee8-c5a5-4033-be57-d7103efccaf3 2013-08-27 11:54:57.668 UTC a93fd4dd-d6bd-4cab-9c6f-9cf972bf6ed1 2011-07-28 14:15:05.728 UTC 7d7576fa-cd04-450f-af43-9dc238cb16b5 2011-08-04 09:03:42.563 UTC c9c8f8d2-7682-4e41-bfeb-b86e05da90c2 2013-11-02 15:13:57.88 UTC aaf7637e-6e6a-46ed-9ab6-669addac25a3 2013-11-02 15:10:26.919 UTC c8f121c5-fc6f-4924-b2dd-04a5ecbbed44 2013-08-30 09:25:14.304 UTC 8f1e1662-ac0c-4125-812b-bafceed923c1 2013-10-31 16:05:18.849 UTC e68d1b72-9b41-4364-bebe-6ec9217fb675 2011-07-28 14:17:06.273 UTC c330027d-38cb-4194-aa20-1ee18dd0e617 2013-02-05 16:18:51.699 UTC 829dfc26-72b5-4fd0-bc6f-a3ed3edfb78b 2013-08-30 08:16:36.778 UTC dc7090e1-65be-4659-a7c0-0c2207579888 2013-06-28 12:43:16.477 UTC 87f5fff0-718b-467c-bb11-0debee6b92b5 2011-08-04 09:04:39.414 UTC 9bb935e1-8929-4b72-a4b4-7609bae026a4 2013-11-02 15:09:54.217 UTC e2667041-2a7d-4c95-8c1c-39d5a984ff4d 2013-08-30 08:24:05.0 UTC This workflow uses the array express library to download data from the array express repository and creates two separate files. The gene expression and the phenotype files. The files are saved in the directory that the user has to specify in the input. NOTE: The library(ArrayExpress) is a prerequisite for this workflow 2013-11-02 15:13:55.341 UTC 936f6342-99ed-4158-a209-82039f583a72 2011-07-28 14:20:51.897 UTC bafdb919-0beb-4f27-947e-3cb7bf9778ea 2013-11-02 14:06:59.642 UTC Eleni Mina 2013-08-30 08:20:34.404 UTC 716ea893-5bdd-46ff-b5e4-8b532ab45909 2011-07-29 14:03:27.629 UTC cacaccc8-a7fe-4dec-b7b8-c0e03db9d364 2013-08-30 08:20:06.844 UTC dbf34938-7ad8-41c4-811c-2ae744c21225 2013-08-30 09:20:38.606 UTC 4cfab05e-634e-4b1c-848c-f444c6c5e7da 2013-08-30 09:26:50.151 UTC 48706bcf-dcbf-4a40-80fd-05c3754c12f9 2013-08-27 11:56:29.707 UTC 543486f6-29e9-42b1-893b-143a138d52a4 2013-08-30 08:19:57.457 UTC a83d1155-1690-499d-80cb-40c71307f592 2013-02-05 18:23:00.82 UTC f6688491-d0e1-414c-97e6-f7a1ee82573e 2011-08-03 13:45:14.852 UTC bab9812d-acbe-4eb7-9832-167b5ab717ca 2011-07-29 15:07:16.639 UTC afb9cb63-f76a-43bc-aa9a-025e2e721164 2013-11-02 14:18:07.158 UTC