[BioC] LIMMA package - coefficient not estimable
yeeling chong
yeelingchong at gmail.com
Fri Mar 30 14:09:41 CEST 2012
Dear Lists,
I'm currently using LIMMA package to analyze my microarray datasets.
For each treatment, I have three biological replicates. The subset of
the constructed design look like this:
Array
R16A R16B R16C R16D R16E S03A ------ Biorep1 Biorep2 Biorep3
02152012_462157_A01_1613_cy5_R16E 0 0 0 0 1 0 ------ 1 0 0
02152012_462157_A01_161_cy3_R16A 1 0 0 0 0 0 ------ 1 0 0
02152012_462157_A02_81_cy5_R08A 0 0 0 0 0 0 ------ 0 0
02152012_462157_A02_813_cy3_R08E 0 0 0 0 0 0 ------ 1 0 0
02152012_462157_A03_164_cy5_R16B 0 1 0 0 0 0 ------ 1 0 0
02152012_462157_A03_1614_cy3_R16E 0 0 0 0 1 0 ------ 0 1 0
02152012_462157_A04_89_cy5_R08C 0 0 0 0 0 0 0 ------ 0 1
02152012_462157_A04_811_cy3_R08D 0 0 0 0 0 0 ------ 0 1 0
02152012_462157_A05_1611_cy5_R16D 0 0 0 1 0 0 ------ 0 1 0
When I fit my data into lmFit, it doesn't estimate the coefficient of
the third biological replicates. The error msg looks like this:
> Fit=lmFit(norm.dataM,designlm,correlation=corfit$consensus)
Coefficients not estimable: Biorep3
Warning message:
Partial NA coefficients for 22664 probe(s)
Can anyone tell me what's goes wrong my my design? Thanks a lot
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