Background Correct Error
1
0
Entering edit mode
Jason Pear ▴ 90
@jason-pear-2309
Last seen 11.2 years ago
An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070807/ 3e9cbbea/attachment.pl
• 901 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 14 hours ago
United States
Hi Jason, Not sure if this is the problem, but your affy and affyio packages are slightly out of date. Try library(Biobase) repos <- biocReposList() update.packages(repos=repos, ask=FALSE) and see if that fixes things. Best, Jim Jason Pear wrote: > Dear List, > > I am new in this field, and I currently faced this error when I tried the > mas5 and gcrma functions. I really appreciate your helps. > > Here are the partial R codes and error messages: > > > # --------------------------------------- > >> mas5.expSet <- mas5(celData); > > background correction: mas > > PM/MM correction : mas > > expression values: mas > > background correcting...Error in as.vector(data) : NA/NaN/Inf in foreign > function call (arg 1) > > > >> gcrma.expSet <- gcrma(celData); > > Adjusting for optical effect.....Done. > > Computing affinities.Error in matrix(NA, nrow = max(cbind(pmIndex, > mmIndex)), ncol = 1) : > > matrix: invalid 'nrow' value (too large or NA) > > > >> sessionInfo() > > R version 2.5.0 (2007-04-23) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > "datasets" "methods" "base" > > > > other attached packages: > > citrusprobe citruscdf LPE affycoretools annaffy > xtable biomaRt RCurl XML GOstats Category > > > "1.16.0" "1.16.0" "1.10.0" "1.8.0" "1.8.1" > "1.4-6" "1.10.0" "0.8-0" "1.7-1" "2.2.5" "2.2.3" > > > Matrix lattice genefilter survival KEGG > RBGL annotate GO graph limma gcrma > > "0.99875-1" "0.15-4" "1.14.1" "2.31" "1.16.0" " > 1.12.0" "1.14.1" "1.16.0" "1.14.2" "2.10.5" "2.8.1" > > > matchprobes affydata affy affyio Biobase > "1.8.1" "1.11.2" "1.14.1" "1.4.0" "1.14.0" > > Many thanks, > > Jason > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician 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: 1588 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