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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