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

[Dick Beyer]

Hi Ting-Yuan,

I started a new session of R and was unable to reproduce my own error.  Even though the packages are the same.  Most strange.

I am very sorry you and Crispin Miller had to bother with this, and thanks for solving my problem, operator error.

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
*******************************************************************************

On Thu, 28 Jul 2005, Ting-Yuan Liu (FHCRC) wrote:

>
> 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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>