Dear list, I have just performed an analysis on a set of hugene2.1 arrays. I have normalised them using RMA method and have done statistical analysis using limma. I found that probesets for same gene have exactly the same expression values and I wonder if anyone can explain. Here one example. Values from the normalised expressionSet for a few of the samples Probeset.ID Sample1 Sample2 Sample3 Sample4 Sample5 Sample6 17017979 9.71251093382803 10.0024198453553 10.1431406981423 10.4515608924303 10.3890663027479 10.6017676219535 17027144 9.71251093382803 10.0024198453553 10.1431406981423 10.4515608924303 10.3890663027479 10.6017676219535 17029788 9.71251093382803 10.0024198453553 10.1431406981423 10.4515608924303 10.3890663027479 10.6017676219535 17032476 9.71251093382803 10.0024198453553 10.1431406981423 10.4515608924303 10.3890663027479 10.6017676219535 17034791 9.71251093382803 10.0024198453553 10.1431406981423 10.4515608924303 10.3890663027479 10.6017676219535 17037271 9.71251093382803 10.0024198453553 10.1431406981423 10.4515608924303 10.3890663027479 10.6017676219535 17039977 9.71251093382803 10.0024198453553 10.1431406981423 10.4515608924303 10.3890663027479 10.6017676219535 Values from the limma differential expression results, excluding AvgExpr column which also shows same value: ID logFC P.Value adj.P.Val Gene Description 17017979 0,274433596 0,000514141 0,275536509 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) 17027144 0,274433596 0,000514141 0,275536509 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) 17029788 0,274433596 0,000514141 0,275536509 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) 17032476 0,274433596 0,000514141 0,275536509 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) 17034791 0,274433596 0,000514141 0,275536509 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) 17037271 0,274433596 0,000514141 0,275536509 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) 17039977 0,274433596 0,000514141 0,275536509 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) Any suggestions will be greatly appreciated Best, Dave [[alternative HTML version deleted]]

Hi David, It's pretty easy to explain. The probesets for this gene are all the same. In other words, the probesets for this gene (except for probeset 17042487) are made up of the exact same 36 probes. > librarypd.hugene.2.0.st) > library(hugene20sttranscriptcluster.db) > prbids <- select(hugene20sttranscriptcluster.db, "6890","PROBEID", "ENTREZID") > dat <- lapply(prbids[1:7,2], function(x) dbGetQuery(con, paste("select fid from pmfeature inner join core_mps on core_mps.fsetid=pmfeature.fsetid where core_mps.meta_fsetid='", x, "';", sep = ""))) > dat2 <- do.call("cbind", dat) > apply(dat2, 1, function(x) length(unique(x))) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 27 28 29 30 31 32 33 34 35 36 1 1 1 1 1 1 1 1 1 1 Best, Jim On 2/14/2014 5:13 AM, David wrote: > Dear list, > > I have just performed an analysis on a set of > hugene2.1 arrays. I have normalised them using RMA method and have done > statistical analysis using limma. I found that probesets for same gene > have exactly the same expression values and I wonder if anyone can > explain. > > Here one example. > > Values from the normalised expressionSet for a few of the samples > > Probeset.ID Sample1 Sample2 Sample3 Sample4 Sample5 Sample6 > 17017979 9.71251093382803 10.0024198453553 10.1431406981423 10.4515608924303 10.3890663027479 10.6017676219535 > 17027144 9.71251093382803 10.0024198453553 10.1431406981423 10.4515608924303 10.3890663027479 10.6017676219535 > 17029788 9.71251093382803 10.0024198453553 10.1431406981423 10.4515608924303 10.3890663027479 10.6017676219535 > 17032476 9.71251093382803 10.0024198453553 10.1431406981423 10.4515608924303 10.3890663027479 10.6017676219535 > 17034791 9.71251093382803 10.0024198453553 10.1431406981423 10.4515608924303 10.3890663027479 10.6017676219535 > 17037271 9.71251093382803 10.0024198453553 10.1431406981423 10.4515608924303 10.3890663027479 10.6017676219535 > 17039977 9.71251093382803 10.0024198453553 10.1431406981423 10.4515608924303 10.3890663027479 10.6017676219535 > > > Values from the limma differential expression results, excluding AvgExpr column which also shows same value: > ID logFC P.Value adj.P.Val Gene Description > 17017979 0,274433596 0,000514141 0,275536509 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) > 17027144 0,274433596 0,000514141 0,275536509 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) > 17029788 0,274433596 0,000514141 0,275536509 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) > 17032476 0,274433596 0,000514141 0,275536509 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) > 17034791 0,274433596 0,000514141 0,275536509 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) > 17037271 0,274433596 0,000514141 0,275536509 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) > 17039977 0,274433596 0,000514141 0,275536509 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) > > Any suggestions will be greatly appreciated > > Best, > > Dave > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099