Hi All,

For a while I have been using these lines below to normalize a large Affy
data set with customCDFs and gcrma. I can't seem to make it work anymore.
For some reason, in the affinity adjustment of gcrma, there is a switch to
the affy CDF which gives an error later. Its a bit puzzling. I am confident
the cdf name is correct and I even updated the custom CDFs to version 14. I
am running R 2.12 and bioconductor 2.7 on a Mac.

Can anyone suggest a solution to this?

Thanks,

Yair


#This is my code

library(affy)

library(gcrma)

options(pkgType="source")

filenames<-as.character(read.table("../CEL-FileNames3.txt", header=FALSE)[,1
])

eset <- just.gcrma(filenames, cdfname="hgu133plus2hsentrezg", optimize.by=
"memory")

data<-as.matrix(exprs(eset))

save(data,file="/tmp/gcrma.normalized.Rbin")



This is the error


   Computing affinitiesLoading required package: AnnotationDbi

.Done.

Adjusting for optical effect..trying URL '
http://bioconductor.org/packages/2.7/data/annotation/src/contrib/hgu133plus2cdf_2.7.0.tar.gz
'

Content type 'application/x-gzip' length 4368753 bytes (4.2 Mb)

opened URL

==================================================

downloaded 4.2 Mb


* installing *source* package ‘hgu133plus2cdf’ ...

** R

** data

** preparing package for lazy loading

** help

*** installing help indices

** building package indices ...

** testing if installed package can be loaded


* DONE (hgu133plus2cdf)


The downloaded packages are in

‘/private/var/folders/hZ/hZWLtN7HGfSpd3FVoI8FFk+++TI/-Tmp-/RtmpfUFkFm/downloaded_packages’

..........

> source("/Volumes/DataHD/BittnerDataset/RunNormalization.r")

Computing affinities.Done.

Adjusting for optical effect........................Done.

Adjusting for non-specific binding.Error in pms[, i] <-
bg.adjust.fullmodel(pms[, i], mm, ncs = NULL, pm.affinities,  :

  number of items to replace is not a multiple of replacement length

In addition: Warning messages:

1: In log(mms) - mu.mm :

  longer object length is not a multiple of shorter object length

2: In mu.pm + rho * (log(mms) - mu.mm) :

  longer object length is not a multiple of shorter object length

3: In x - bhat :

  longer object length is not a multiple of shorter object length

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