[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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