Problems with justGCRMA: Error in bg.adjust.fullmodel
1
0
Entering edit mode
@jordi-altirriba-gutierrez-682
Last seen 3.5 years ago
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",optim ize.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="memo ry",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)
vsn gcrma matchprobes plier vsn gcrma matchprobes plier • 540 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States
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 Guti?rrez 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",opti mize.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="me mory",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) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- 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
ADD COMMENT

Login before adding your answer.

Traffic: 360 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6