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List:       bioconductor
Subject:    [BioC] Unable to read GPR files for LIMMA
From:       Guoneng Zhong <guoneng.zhong () yale ! edu>
Date:       2005-05-25 18:00:00
Message-ID: 4294BD20.9070109 () yale ! edu
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Hi,

read.maimages seems to be fine reading five GPR (1.3) files.  But when I 
tried to correct for backgrond, I get this:

 RG <- backgroundCorrect(RG,method='normexp')
Corrected array 1
Corrected array 2
Corrected array 3
Corrected array 4
Error in optim(c(beta, log(sigma), log(alpha)), sumloglik, gr = 
grsumloglik,  :
        non-finite value supplied by optim


So I ignored the background and went ahead with normalization (default 
one as well as loess), and did a lmFit.  So far so good, but then when I 
tried with eBayes, I get this warning message:

 > fit<-eBayes(fit)
Warning message:
Estimation of var.prior failed - set to default value in: ebayes(fit = 
fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim)

So is there something wrong with the image files?  if so, how do I know 
what it is?

Thanks,
g


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