Hi,

I'm using R2.3.1 and Bioconductor 1.8 (I think, but am not sure how to
check). I'm getting warning message that I have not found described in the
mailing list archives or in the help for eBayes and was hoping someone could
help.

Here's the relevant background output, minus a filter function called
filters that I defined but have left out here for brevity:
-------------------------------------------------------------
> targetsA <- readTargets("targetsA.txt")

> targetsA
     SlideNumber FileName  Cy3  Cy5
A296           1 A296.gpr DH1C DH1D
A297           2 A297.gpr DH1C DH1D
A298           3 A298.gpr DH1D DH1C
A299           4 A299.gpr DH1D DH1C

> RGAn= read.maimages(targetsA$FileName, source="genepix", wt.fun=filters,
other.columns=c("F635 SD",
+ "B635 SD", "F532 SD", "B532 SD", "F Pixels", "B Pixels", "B532 Mean","B635
Mean","% > B635+2SD", "% > B532+2SD"))
Read A296.gpr
Read A297.gpr
Read A298.gpr
Read A299.gpr
> RGAn <- normalizeBetweenArrays(RGAn, method="scale")

> designmatrix <- modelMatrix(targetsA, ref="DH1C")
Found unique target names:
 DH1C DH1D

> designfitA <- lmFit(RGAn, design=designmatrix, method="ls")

> contrastfitA <- eBayes(designfitA)

Warning message:
Zero sample variances detected, have been offset
------------------------------------------------------------------------
Do I need to worry about this message? Things downstream seem to be working,
but appearances are sometimes deceptive.

Thanks,

Matt


-- 
Matt Scholz
Senior Research Specialist
Department of Plant Sciences
University of Arizona

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