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From: Hervé L. <her...@in...> - 2015-09-01 16:41:27
|
Dear all, I have been exploring the scripting option on TMEV to run pipeline of analysis. I get issues as my primary data do not get transformed by adjustement algorithms. I could not find any online FAQ to fix this or try to understand what I am doing wrong. I know TMEV is not supported anymore but it has been very useful to our current work in multiparameter flow data analysis. Having this scripting option working reliably woul dbe a big plus. So I hope any of TMEV developper is still around to help us on that. Thanks for your help in advance, Hervé -- -- Vous utilisez la version libre et gratuite d'OBM, développée et supportée par Linagora. Contribuez à la R&D du produit en souscrivant à une offre entreprise. http://pro.obm.com/ - http://www.linagora.com |
From: Valeria P. P. <vpa...@uo...> - 2014-01-08 20:30:50
|
Hi I am trying to run EdgeR analysis on my RNAseq data and I get this msgs in my windows and mac computer: Win 7, MeV4_9_0 Rpack i386 3.0.2 java.lang.ClassCastException: org.tigr.microarray.mev.SlideDataElement cannot be cast to org.tigr.microarray.mev.RNASeqElement at org.tigr.microarray.mev.RNASeqSlideData.getCount(RNASeqSlideData.java:29) at org.tigr.microarray.mev.cluster.gui.impl.edger.EDGERGUI.execute(EDGERGUI.java:211) at org.tigr.microarray.mev.MultipleArrayViewer$7.run(MultipleArrayViewer.java:2625) at java.lang.Thread.run(Unknown Source) Mac 10.7.5, R package 3.0.2 MeV: 4_8_1 java.lang.ClassCastException: org.tigr.microarray.mev.SlideDataElement cannot be cast to org.tigr.microarray.mev.RNASeqElement at org.tigr.microarray.mev.RNASeqSlideData.getCount(RNASeqSlideData.java:29) at org.tigr.microarray.mev.cluster.gui.impl.edger.EDGERGUI.execute(EDGERGUI.java:211) at org.tigr.microarray.mev.MultipleArrayViewer$7.run(MultipleArrayViewer.java:2625) at java.lang.Thread.run(Thread.java:695) Could you please somebody help me with that? Thanks in advance, VP |
From: <Dor...@fa...> - 2013-08-28 18:31:51
|
I have affymetrix human gene 1.0 microarray data from a time course series containing both controls and experimental subjects results. How can I use MeV to analyze the output from RMA or from the CEL files? Doris M. Kupfer, Ph.D. Research Geneticist Civil Aerospace Medical Institute, AAM-610 Federal Aviation Administration 6500 S. MacArthur Blvd. Oklahoma City, OK 73169 405-954-7512 dor...@fa... |
From: Kim C. <kx...@bh...> - 2011-01-25 16:04:44
|
Dear All, In the implentation of the BETR algorithm published by the authors they use Storey's FDR method for multiple testing correction. I was wondering if any of you know if this is also implemented in MeV, the reason I ask is because in the general info after you've finished a BETR run it says Correction: just alpha (no correction). Can anyone confirm either way, I suspect BETR has been implemented in full but it would be great to be 100% sure. Thanks in advance, Kim |
From: chunjiang he <cam...@gm...> - 2010-10-05 17:40:43
|
Dear Mr/Ms, I encountered a problem when i run TM4 on windows vista x32, it said out of memory. So I changed the TMeV.bat line: java -Djava.library.path=lib -Xss1M -Xmx512m -cp %ClassPath% org.tigr.microarray.mev.TMEV I change the memory 512 to 2048 or 1024, but the TMeV cannot be started. When I change the memory back to 512, then it works. I dont know what is the problem. Is it java installation problem? I reinstalled the java platform, but it is the same. Thanks very much. Chunjiang University of Chicago |
From: Eleanor H. <ele...@ji...> - 2009-07-27 16:11:36
|
Hi Peng, We don't do much with this mailing list anymore, so I took the liberty of posting your question on the SourceForge help forums for MeV at https://sourceforge.net/forum/message.php?msg_id=7529963 . I also posted what I hope is a useful answer. Eleanor Peng Yu wrote: > Hi, > > I am new to MeV. Please bear with me if my question is primitive. I > have the following normalized expression level file. ko* are for the > knock out cases. wt* are for the control cases. I am wondering what > the procedure I should follow to compute the list of differentially > expressed genes. Can somebody help me? > > $ head output.txt > koA-mth_HZ_5238_MST1_19389.cel koB-mth_HZ_5238_MST1_19390.cel > koC-mth_HZ_5238_MST1_19391.cel koD-mth_HZ_5238_MST1_19392.cel > wt1-mth_HZ_5238_MST1_19385.cel wt2-mth_HZ_5238_MST1_19386.cel > wt3-mth_HZ_5238_MST1_19387.cel wt4-mth_HZ_5238_MST1_19388.cel > 10344615 7.07210987006919 7.01089258722033 > 7.2642627000072 6.92980486555595 7.72857978063884 > 6.91124431275741 7.45776182961327 7.21025349865986 > 10344617 3.02519545040591 3.08697023169755 > 3.03203234085828 3.09846420636071 3.12487891156704 > 3.10727683101607 3.0544609560487 3.03353963677405 > 10344619 3.20294677833793 3.20612630466463 > 3.17655303153672 3.13210443165341 3.1378507207366 3.21452663497659 > 3.31345050224224 3.09287042099817 > 10344621 4.70984671316916 4.68863215464979 > 4.43705857330756 4.59970839525133 4.66911715996711 > 4.80422412543456 4.57334787499862 4.60736276830484 > 10344623 7.79927399492793 7.78057650451938 > 7.72710416870418 7.68525205462879 7.66271776323834 > 7.65761154201622 7.67860029345257 7.80684426781102 > 10344625 8.43869623252839 9.23986002214653 > 9.01482181726202 8.8450593076064 8.59194370149885 > 9.08344656110017 9.07468813004613 8.92291936928794 > 10344626 10.0590964382247 9.75778614016683 > 9.66874458340189 9.91560261746937 9.97497585580347 > 9.90593250683953 9.72513220186519 10.0570156812405 > 10344627 7.45353674141328 7.85528510695415 > 7.1239938834144 7.48673272391552 8.2401362665769 7.24092300626232 > 7.4348487408975 7.8999935331867 > 10344628 10.1181530678991 10.2050144957479 > 10.0821326432175 10.2014962484731 10.3549307008668 > 9.97359523972773 9.82152593658235 10.0714458425003 > > > Regards, > Peng > > ------------------------------------------------------------------------------ > _______________________________________________ > mev-tm4-users mailing list > mev...@li... > https://lists.sourceforge.net/lists/listinfo/mev-tm4-users > |
From: Peng Yu <pen...@gm...> - 2009-07-26 20:23:59
|
Hi, I am new to MeV. Please bear with me if my question is primitive. I have the following normalized expression level file. ko* are for the knock out cases. wt* are for the control cases. I am wondering what the procedure I should follow to compute the list of differentially expressed genes. Can somebody help me? $ head output.txt koA-mth_HZ_5238_MST1_19389.cel koB-mth_HZ_5238_MST1_19390.cel koC-mth_HZ_5238_MST1_19391.cel koD-mth_HZ_5238_MST1_19392.cel wt1-mth_HZ_5238_MST1_19385.cel wt2-mth_HZ_5238_MST1_19386.cel wt3-mth_HZ_5238_MST1_19387.cel wt4-mth_HZ_5238_MST1_19388.cel 10344615 7.07210987006919 7.01089258722033 7.2642627000072 6.92980486555595 7.72857978063884 6.91124431275741 7.45776182961327 7.21025349865986 10344617 3.02519545040591 3.08697023169755 3.03203234085828 3.09846420636071 3.12487891156704 3.10727683101607 3.0544609560487 3.03353963677405 10344619 3.20294677833793 3.20612630466463 3.17655303153672 3.13210443165341 3.1378507207366 3.21452663497659 3.31345050224224 3.09287042099817 10344621 4.70984671316916 4.68863215464979 4.43705857330756 4.59970839525133 4.66911715996711 4.80422412543456 4.57334787499862 4.60736276830484 10344623 7.79927399492793 7.78057650451938 7.72710416870418 7.68525205462879 7.66271776323834 7.65761154201622 7.67860029345257 7.80684426781102 10344625 8.43869623252839 9.23986002214653 9.01482181726202 8.8450593076064 8.59194370149885 9.08344656110017 9.07468813004613 8.92291936928794 10344626 10.0590964382247 9.75778614016683 9.66874458340189 9.91560261746937 9.97497585580347 9.90593250683953 9.72513220186519 10.0570156812405 10344627 7.45353674141328 7.85528510695415 7.1239938834144 7.48673272391552 8.2401362665769 7.24092300626232 7.4348487408975 7.8999935331867 10344628 10.1181530678991 10.2050144957479 10.0821326432175 10.2014962484731 10.3549307008668 9.97359523972773 9.82152593658235 10.0714458425003 Regards, Peng |