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David A.
▴
70
@david-a-4430
Last seen 10.1 years ago
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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