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

[Dick Beyer]

Hi Crispin,

Thanks for looking into this.  I will have to wait until the windows version of 2.1.3 is available.

Thanks 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
*******************************************************************************

On Wed, 27 Jul 2005, Crispin Miller wrote:

> Hi,
> This is interesting... I've tried to duplicate this with 2.1.3 from the
> devel library and the current release version and it works fine for me
> on windows and on linux. Please can you try updating to 2.1.3 and seeing
> if that fixes things?
> If not then let me know and we can try to explore things further.
> Best,
>
> Crispin
>
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Dick Beyer
> Sent: 27 July 2005 00:33
> To: Bioconductor
> Subject: [BioC] zebrafish simpleaffy Error in FUN(X[[4]], ...) :
> subscript out of bounds
>
> 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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