[BioC] problems with gcrma just.gcrma

Elisabetta Manduchi manduchi at pcbi.upenn.edu
Mon Dec 4 23:02:31 CET 2006


Hello,
I'm trying to use just.gcrma with data from Affy MGU74Av2 and am getting 
the error at the bottom of what's copied below re read.probematrix. I'm 
running version 2.4.0 of R and gcrma version 2.6.0. The mgu74av2 packages 
being downloaded are version 1.14.0.
Can anybody advice on what I can do to overcome this?
Thanks,
Elisabetta
---
> data.gcrma<-just.gcrma(filenames=cel.files, type=c("fullmodel"), normalize=T, optimize.by=c("memory"), fast=T, samepleNames=sample.names)

Computing affinities[1] "Checking to see if your internet connection 
works..."
trying URL 
'http://bioconductor.org/packages/1.9/data/annotation/bin/windows/contrib/2.4/mgu74av2cdf_1.14.0.zip'
Content type 'application/zip' length 1340750 bytes
opened URL
downloaded 1309Kb

package 'mgu74av2cdf' successfully unpacked and MD5 sums checked

The downloaded packages are in
         C:\Documents and Settings\Elisabetta Manduchi\Local 
Settings\Temp\Rtmpc7v1qb\downloaded_packages
updating HTML package descriptions
[1] "Checking to see if your internet connection works..."
trying URL 
'http://bioconductor.org/packages/1.9/data/annotation/bin/windows/contrib/2.4/mgu74av2probe_1.14.0.zip'
Content type 'application/zip' length 2396326 bytes
opened URL
downloaded 2340Kb

package 'mgu74av2probe' successfully unpacked and MD5 sums checked

The downloaded packages are in
         C:\Documents and Settings\Elisabetta Manduchi\Local 
Settings\Temp\Rtmpc7v1qb\downloaded_packages
updating HTML package descriptions
.Done.
Error in read.probematrix(filenames = filenames, which = "pm", cdfname = 
cdfname) :
         VECTOR_ELT() can only be applied to a 'list', not a 'symbol'
---



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