[BioC] Problems with justGCRMA: Error in bg.adjust.fullmodel

[James W. MacDonald]

Hi Jordi,

You need to update your gcrma package to 1.1.4 - several variables have 
been removed from bg.adjust.fullmodel() and the fix for justGCRMA() is 
in the newest version of gcrma.

Best,

Jim



Jordi Altirriba Gutiérrez wrote:
> Dear users,
> I’m trying to obtain the GCRMA expression values of 26 Affymetrix 
> microarrays (HGU133plus2). Due to a limitation of RAM (2Gb), I can’t use 
> GCRMA directly:
> 
> Data<-ReadAffy()
> esetGCRMA<-GCRMA(Data)
> 
> So I’m trying to do it with justGCRMA, but I’m obtaining this error:
> 
> 
>>esetGCRMA<-justGCRMA(filenames=list.celfiles(),type="fullmodel",optimize.by="memory",fast=TRUE)
> 
> Computing affinities..Done.
> Adjusting for optical effect...........................Done.
> Adjusting for non-specific binding.Error in bg.adjust.fullmodel(pms[, i], 
> mm, pm.affinities, mm.affinities,  :
>         unused argument(s) (Q ...)
> 
> I’ve also tried with 
> just.gcrma(filenames=list.celfiles),type="fullmodel",optimize.by="memory",fast=TRUE)
> 
> But I’m obtaining the same error.
> 
> The data of my computer and R:
> PC: Intel centrino M 2GHz
> OS: Windows XP pro
> 
> R version 2.1.0, 2005-06-02, i386-pc-mingw32
> 
> attached base packages:
> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"  
> "datasets"  "base"
> 
> other attached packages:
>         vsn       plier       gcrma matchprobes        affy  reposTools
>     "1.6.3"     "1.0.0"     "1.1.3"    "1.0.22"     "1.6.7"    "1.5.19"
>     Biobase
>    "1.5.12"
> 
> Any help will be very much appreciated.
> 
> Thanks for your time
> 
> Jordi Altirriba
> PhD student
> Hospital Clinic (Barcelona, Spain)
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623