[BioC] Different probesets but same expression values?

[James W. MacDonald]

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.

 > library(pd.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
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099