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

[Ting-Yuan Liu (FHCRC)]

Hi Dick,

Could you provide more information about your code?  I try to reproduce 
the error, but I cannot.  I don't know how you created the AffyBatch 
object "all.raw".  If you can provide the complete code, it will be 
helpful.

Ting-Yuan

On Tue, 26 Jul 2005, Dick Beyer wrote:

> 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
> 
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