[BioC] Vsn and rma with PM only arrays

Roumyana Yordanova roumyana.yordanova at bms.com
Wed May 7 18:57:19 CEST 2008

Unfortunately the data are confidential so I can not send an example.
Actually, the problem is in the summarization. Both vsn2 and rma work 
for the background and normalziation part but failed for the median 
polish algorithm.
I can do all the steps separately (using pmindex in the last part to do 
the summary only for pm) and then everything works.

Is there any opiton in rma (vsn) that specify use pm only for the 
summary, i.e. skip an estimation of mm(x). Actually the last command 
gives the error.


Wolfgang Huber wrote:

> Roumyana Yordanova wrote:
>> I am trying to use rma or vsn on PM arrays (in particular Mouse 430).
>> Both stoped with an "error in .local(object,...) : subscript out of 
>> bounds".
>> (mmindex returns 0 for all probes. Is this the right coding for PM 
>> arrays or this is the problem?).
>> Thanks for any help.
>> Roumyana
> Dear Roumyana,
> please send a reproducible example (R script, using data that we can 
> access as well), the output of sessionInfo() and the exact error 
> message you get. Then I or someone might be able to help.
> Best wishes
>   Wolfgang
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

More information about the Bioconductor mailing list