Get_differentially_eexprs_file00Location of the gene expression data2013-02-10 13:37:25.683 UTCphenotypeData00Location of the phenotype data2013-02-10 13:37:05.497 UTCcf00This input port takes an integer 1 or 2 or 3, which represents the first, second or third coefficient that we want to export from top table (limma), when we test for differential expression.
We tested for DE between HD and normal tissue in each brain region. Therefore
cf = 1 -> caudate nucleus
cf = 2 -> frontal lobe
cf = 3 -> cerebellum2013-02-10 13:36:30.70 UTCworking_dir00the desired working directory. This workflow saves the results in .txt files and therefore
its useful for the user to provide a directory to save the results in.2013-08-27 14:12:05.873 UTC\tmp\2013-08-27 14:12:11.648 UTCfilename_gene_idsfile_DE_genesget_necessary_filesphenotype_file0expression_file0datadirectory0Loads the files we defined at the input ports. Gene expression and phenotypic data2013-02-10 14:05:23.668 UTCnet.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivityexpression_file0falsephenotype_file0falsedatadirectory0falsefalselocalhost6311truefalseexpression_fileTEXT_FILEphenotype_fileTEXT_FILEdatadirectorySTRINGnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_expression_setprobe_ids11create expression set object to be used by limma to test for DE2013-02-10 14:05:38.36 UTCnet.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivityout100probe_ids11falselocalhost6311truefalseout1STRINGprobe_idsSTRING_LISTnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokelibrariesLoad necessary libraries.
If not existing libraries need to be installed beforehand.
these are :
library(ArrayExpress)
library(hgu133b.db)
library(limma)2013-02-10 14:07:31.61 UTCnet.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivityfalselocalhost6311truefalsenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecompute_DE_limmanet.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeprobenames_to_entrez_genes_ids_Array_Bprobe_ids_new1translates probe names to entrez gene ids. For array B. 2013-02-10 14:05:56.986 UTCnet.sf.taverna.t2.activitiesrshell-activity1.4net.sf.taverna.t2.activities.rshell.RshellActivityprobe_ids_new1falsefalselocalhost6311truefalseprobe_ids_newSTRING_LISTnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_DE_genescf0cut_off0filename00file_DE00net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecut_offvalue00cut_off value for exporting DE genes.
Here it is defined as 0.05. for other p value cut offs this constant needs to be changed
2013-02-10 14:19:52.532 UTCnet.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity0.05net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeget_necessary_filesphenotype_fileget_necessary_filesexpression_fileget_necessary_filesdatadirectoryprobenames_to_entrez_genes_ids_Array_Bprobe_ids_newget_DE_genescfget_DE_genescut_offfilename_gene_idsfile_DE_genes5548d9c9-bd5f-4fc6-837b-4fe9935ec7072013-02-06 11:34:02.629 UTC7a09762a-2c68-43d3-87a2-70c5e8f73c662013-02-09 19:57:32.282 UTC22e9b9eb-b92e-460f-9622-7f1aff96981e2013-02-05 15:44:58.356 UTC2a7471db-928a-49f6-a66a-a5b685b3780e2013-02-10 12:17:08.782 UTC4cf63f2d-4be2-4307-b350-4069a29826872013-02-10 13:23:28.974 UTC0563dc4b-563c-472f-81e3-c08ffcdee6982013-02-09 18:45:41.407 UTC68cdc139-59b3-4b2f-8c8b-2ca5a6a6ed4f2013-02-10 14:15:48.191 UTC8b237bf5-d9e7-48c2-97e5-6c1557b7776f2011-10-24 07:40:00.69 UTCba813f0b-1c79-47da-b1d6-4fe64ca37f6f2013-02-09 20:09:43.841 UTC74c24a75-440e-447c-b74b-8e47eaace0572013-02-10 14:17:09.844 UTC53aa8f13-6638-421e-81a1-903a7d6d4a462013-02-10 13:28:05.729 UTCd77fadfc-f7c4-44ee-9f8a-3184c080c1bc2011-07-27 12:37:40.664 UTC9f7c4c7b-2760-48ee-96d9-778fdeae25be2013-02-09 17:11:00.288 UTCccab3dc0-0ae0-46ed-984b-46cbf0bb2ac52013-08-27 15:00:07.27 UTC38b14968-3465-48ea-938a-bdf33e7ae4f02013-02-09 17:06:41.237 UTC28859247-6fe1-4abb-b57d-aa44019db2dc2013-02-09 20:18:59.440 UTCd1f41a7e-b2b3-4114-ad64-17b200b78c872013-02-07 18:09:09.926 UTC8b5c0f8d-4e68-46e9-b021-662a87ef3d582013-02-07 15:05:00.772 UTCc82cf035-b66f-436a-a223-38176e2c13d02013-02-09 17:08:26.193 UTC46c42f3a-3fdd-4c05-845b-5d4326d07d752011-07-27 13:13:06.705 UTCe88bd9ca-0442-41a1-82c6-6fc78c16ff782011-07-27 11:22:13.130 UTC06effb2a-395d-4df7-9773-2b7e81cf7ccb2013-02-10 13:47:13.2 UTC50f7c15b-5709-4662-b0f5-d6408b2ece962013-02-09 20:24:33.757 UTCa5ed14bd-8d64-4bbf-8a5c-c4ac54df6ce72011-07-27 12:20:53.487 UTC71415f02-1d87-47fe-b9fa-19a3666f8fc02011-10-25 10:50:23.719 UTCc7c541c0-952d-41a9-a08c-95175b6334272013-02-10 13:02:37.12 UTCe19b4e37-533b-4391-8e0d-ea3216fc0aa22013-02-09 18:17:43.403 UTCeb73f4cf-5ff9-4b25-a85d-a26278d80bd72011-07-27 15:44:18.798 UTC4438a443-d190-41df-ae99-770948df13b02011-10-13 09:01:53.267 UTCdd6e9a9b-ead8-4b69-a479-89fc4539b0522011-10-13 08:46:42.298 UTC84c02ba8-1d13-48bf-82ea-af31d92733122013-02-10 14:05:24.723 UTC2cd24e2b-ff49-4276-a08e-b43ab53ee48e2013-02-09 16:09:24.811 UTC0737eae5-079c-401f-a237-21c4ff5668162011-07-27 12:24:40.450 UTCca06ba1e-535e-4450-803d-916c5bb855bd2013-02-09 18:32:54.190 UTC857d309a-99cc-43ee-87af-acc30b26823f2013-02-09 18:25:15.499 UTC****IMPORTANT****:if libraries: library(ArrayExpress), library(hgu133b.db), library(limma) are not installed in the local R installation, then they need to be installed before running this workflow.
Original data come from Hodges et. al 2006 "Regional and cellular gene expression changes in human Huntington’s disease brain"
This workflow loads the two necessary files (gene expression data & phenotype data), and creates the expression set object to be used by the R package limma, to test for DE.
In this example we test for DE between HD and controls for each brain region. To test for DE between other variables, this information can be changed at the workflow "compute_DE_limma"
2013-08-28 15:16:25.568 UTCe71c3dcc-7b96-4e6d-8635-daa729b8b0d22013-02-09 20:21:45.273 UTCa75976a6-aa09-45d6-8555-031f877bf7272013-08-27 15:20:59.239 UTCf589947d-9831-43da-8785-28583092db202013-02-09 16:19:15.570 UTCe5d7cefe-1bb7-43f5-b1a8-e33560e589552011-07-27 12:29:25.597 UTC7c7e892f-8972-4ba2-990f-db556a0e085d2013-02-10 13:49:12.460 UTCe69ac0bb-a3f9-4649-95d7-57c5cc9ff6b22013-02-10 13:37:06.780 UTC7ec37103-e2ee-4a91-b8d2-3f73dd7c93eb2011-10-19 18:26:57.228 UTCb2509878-da0e-4a0e-b492-998db9c5c0fb2013-02-10 11:01:06.530 UTC5f9292b9-fffb-44ef-9697-004505a8fd452011-07-27 11:23:54.423 UTC02ef7030-4e2c-4167-8f92-53637a130a972013-02-09 18:43:35.627 UTCd1634299-0fd9-4913-9805-7c77be8ca49b2013-02-10 14:22:26.288 UTC265af27e-8eb2-48d5-a9d2-8805f5dd662a2013-02-09 19:31:00.912 UTC1b0bf25c-eef8-4fc9-b08a-b97f5fbd7fce2013-02-05 18:24:48.878 UTC03179cd5-0e09-4a1a-b2d8-1f5eea946cf72011-10-24 07:36:54.639 UTC84ec68c4-533c-4da0-a492-f87defa9921a2013-02-10 13:45:22.103 UTC34a0e230-efaa-4910-945f-8608f6b541b32011-07-27 14:27:59.846 UTC91fde642-56c7-43d5-bcb2-4aa3740c67db2013-02-09 18:30:43.241 UTCab1188e6-8089-473d-8efb-70a18ac5afcc2011-10-19 18:20:25.832 UTC31d1f631-6ee6-49a1-bd23-14fa32a5719a2011-07-27 12:28:32.538 UTC15c9ef40-2422-44a3-9ad6-b5731924f7582013-02-10 10:56:51.918 UTC34a6cff3-2033-4599-884f-7743c535443d2013-02-09 19:38:35.772 UTCGet differentially expressed genes for Array B (one brain region)
2013-02-10 13:46:15.401 UTC3a1d446b-2bcb-4024-a595-f79c1fd6725d2013-02-09 18:27:03.230 UTCda2c79da-4bb8-4f24-a842-d2f2e15ab5842013-02-10 14:08:31.174 UTC5077cacd-aed1-4380-8b39-d5bc1c5fe8412013-02-07 15:08:02.268 UTCf66526ee-833d-4a51-a130-fd972dcb41642011-07-27 10:59:42.981 UTC06eb476e-fe84-4d91-911f-2cfa001436222013-08-27 14:12:10.555 UTC07de2939-df2e-48a1-b0de-5dc0c1e0d7f52011-07-27 13:04:24.867 UTCf3994354-ff08-4a1e-a7fb-84be9ab6805c2013-02-10 14:19:52.614 UTC6c6b960b-fbec-44e8-917d-0526eceb5a332011-10-19 18:30:39.94 UTC1424161d-f78d-4e50-8a47-65eb55eab79b2013-02-10 13:36:35.217 UTCc6c630d9-4b95-4497-8851-7e5b1104a9342013-02-09 18:22:29.750 UTCf78a1474-4ea5-4e92-ad39-d84b07d24f102011-07-27 13:32:09.513 UTC78de8bc6-d7c4-4454-90e1-a2149c323eb12013-02-10 10:51:53.745 UTCa444b8fd-f6cb-4f00-8606-6db1f00df7002011-07-27 14:31:53.366 UTC934dcf9d-3054-4aba-8dda-a141aa7804e92013-02-10 14:05:38.736 UTCEleni Mina2013-02-10 13:42:59.422 UTCec0798f7-25e5-4cc4-9ea7-18349d8ca5852013-02-09 18:53:51.128 UTC537888c0-27e6-4229-aecd-c63d75bf58fa2013-02-07 14:59:08.799 UTCa74868f8-37e9-4800-ba3a-715137c259c92013-02-10 11:06:17.702 UTCe9806396-10ad-46b6-b2f2-49a6f2cf0bec2011-07-27 12:59:24.833 UTC936ab012-1643-4a2e-b301-ac175629e1842011-07-27 13:24:52.237 UTC75e8eb60-e9ae-46d8-9e55-623f22f2b1482013-02-10 13:37:26.846 UTC88de8d8f-fdc9-45a2-a70f-28212f6b874e2013-02-10 10:47:14.945 UTC381cb695-82bb-461f-b7d8-696f6695125a2013-02-06 15:28:21.750 UTC8cdd65c7-4b3c-44cc-b287-3e231824f8a42011-10-24 07:37:59.172 UTCdcaeec7a-2088-4a1d-a87c-ec1580518aef2013-02-09 18:49:36.978 UTC06281a52-a6e7-4acd-aae1-44e3041894452013-02-10 14:05:58.60 UTCc16667f8-75a7-4315-aaea-1beb9e66ead32011-10-19 18:28:46.180 UTCce69f001-c3fc-4846-9da3-d12b9cc266082013-02-09 16:36:49.473 UTCb9094592-489f-4b11-9037-7d8ec4d392312013-02-07 15:11:34.554 UTC42f29aed-be98-442e-8041-2eee91912c142013-02-10 11:01:15.969 UTCab8213df-5d5d-48ca-b319-9328bde073c92013-08-27 14:32:33.119 UTC367b97d8-c7d3-41fc-b645-7d7a2b57bdec2013-02-07 15:05:38.182 UTC54c4445c-d7ac-422a-8f8a-0c3f98ebeb652013-02-09 19:53:25.912 UTC4c3bbd52-245f-4143-bbbb-112e83817d7d2013-08-27 14:53:00.303 UTC29e20d00-da2e-42a0-a63c-7bfa83b6aac12013-02-10 12:28:28.204 UTC5c20b887-e2a2-43f4-9e19-a7fc0334cb522013-02-10 13:03:01.901 UTC33f60dbe-c6ac-4854-b14c-c2c12dc315922013-02-09 19:41:52.995 UTC77b30169-7a25-4934-8833-07158935ec632011-10-13 08:33:44.864 UTC1b5c0647-8a05-4428-be04-d8be0f8ed9812013-02-10 11:53:34.887 UTC3241ac1a-5d92-429a-a965-e5454e6dc5862013-10-31 16:13:36.273 UTCc58c01e5-e73f-45ad-82b7-2c50871b6f4d2013-02-10 14:16:35.343 UTCee48d96b-067d-4ccc-9df7-1268bf77cda32013-02-09 17:13:43.494 UTCd3a61584-5a2e-4224-8804-dfbb2beb5cf62013-02-10 12:48:02.221 UTCb845c4a9-b441-412b-be2e-a8bdbf193ffb2013-02-10 11:53:24.772 UTC051d461f-9481-4d40-accf-225de1875bcc2013-02-09 17:05:59.992 UTC4d9f7945-2fd6-401b-9558-a4199c53c3bb2013-02-09 18:51:04.914 UTC24cc847e-60c0-4beb-bd86-3b5d579defcb2011-10-19 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