I am attempting to use gcrma on AffyBatch objects which were read in
using the "rm.outliers=TRUE" or "rm.mask=TRUE" options (to the ReadAffy
function).  For example, I put two MOE430 CEL files in the working
directory, and here is what I tried:

 

> ab<-ReadAffy(filenames=list.celfiles(),rm.outliers=TRUE)

> ai<-compute.affinities(cdfName(ab))

.> data<-gcrma(ab,ai)       

Adjusting for optical effect..Done.

Adjusting for non-specific binding.Error in
gcrma.bg.transformation.fast(pms, bhat, var.y, k = k) : 

        NAs are not allowed in subscripted assignments

> sessionInfo()

Version 2.3.1 (2006-06-01) 

i386-pc-mingw32 

 

attached base packages:

[1] "splines"   "tools"     "methods"   "stats"     "graphics"
"grDevices"

[7] "utils"     "datasets"  "base"     

 

other attached packages:

mouse4302probe   mouse4302cdf          gcrma    matchprobes
affy 

      "1.10.0"       "1.10.0"        "2.6.0"        "1.4.0"
"1.12.2" 

        affyio        Biobase 

       "1.0.0"       "1.10.1"

 

 

I have tried using both R versions 2.3.1 and 2.1.0, and gcrma versions
1.1.4 and 2.6.0, and affy versions 1.12.2 and 1.10.0.  I get a similar
error when using the rm.mask=TRUE option.  

 

My overall goal is to remove select probes from the analysis (in this
case, probes that overlap known polymorphisms).  Any thoughts on how
best to do this are most appreciated...

 

Cheers,

-andrew 

 

--

Andrew Su, Ph.D.

Genomics Institute of the 

  Novartis Research Foundation

asu@gnf.org

Tel: 858-812-1656

Fax: 858-812-1630

http://web.gnf.org

 


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