[BioC] Background Correct Error

[James W. MacDonald]

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slightly out of date.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]]
> 
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-- 
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