[BioC] Vsn and rma with PM only arrays

lgautier at altern.org lgautier at altern.org
Thu May 8 10:53:37 CEST 2008

> Unfortunately the data are confidential so I can not send an example.

If the output of "sessionInfo()" on your end,
as well as a copy/paste of the error message thrown by R,
are classified it is harder for people to try providing help.

> 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.
> Thanks.
> Roumyana
> 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
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