[BioC] zebrafish simpleaffy Error in FUN(X[[4]], ...) : subscript out of bounds

[Dick Beyer]

I have a problem with simpleaffy and zebrafish:

> all.raw
AffyBatch object
size of arrays=712x712 features (11889 kb)
cdf=Zebrafish (15617 affyids)
number of samples=3
number of genes=15617
annotation=zebrafish

> all.mas5 <- call.exprs(all.raw,"mas5")
Background correcting
Retrieving data from AffyBatch...done.
Computing expression calls... 
...done.
scaling to a TGT of 100 ...
Scale factor for: EG Zebrafish control 20July05.CEL 1.07236539803815 
Scale factor for: EG Zebrafish 310 20July05.CEL 1.14945565186904 
Scale factor for: EG Zebrafish 820 20July05.CEL 1.04463357372716 
> qc <- qc(all.raw,all.mas5)
Getting probe level data...
Computing p-values
Doing PMA Calls
Error in FUN(X[[4]], ...) : subscript out of bounds

> sessionInfo()
R version 2.1.1, 2005-07-10, i386-pc-mingw32

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices"
[6] "utils"     "datasets"  "base"

other attached packages:
zebrafishprobe   zebrafishcdf      zebrafish         qvalue
          "1.1"        "1.5.1"        "1.8.4"          "1.1"
          gcrma    matchprobes     simpleaffy           affy
        "1.1.4"       "1.0.22"        "2.1.1"        "1.6.7"
     reposTools        Biobase
       "1.5.19"       "1.5.12"

Thanks very much,
Dick

*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer