[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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