This seems to be an issue with the way AffyBatch object is created. The 
error is:

 >library(htmg430pmcdf)
 >data <-ReadAffy(filenames=dir())
 >data
AffyBatch object
size of arrays=744x744 features (14 kb)
cdf=HT_MG-430_PM (45163 affyids)
number of samples=6
number of genes=45163
annotation=htmg430pm
notes=

 > mm(data)
Error in .local(object, ...) : subscript out of bounds
In addition: Warning message:
NAs introduced by coercion in: .local(object, ...)

 >mmIndex(data)

------
$`1428469_PM_a_at`
 [1] 0 0 0 0 0 0 0 0 0 0 0
 
$`1428470_PM_at`
 [1] 0 0 0 0 0 0 0 0 0 0 0
 
$`1428471_PM_at`
 [1] 0 0 0 0 0 0 0 0 0 0 0
 
$`1428472_PM_at`
 [1] 0 0 0 0 0 0 0 0 0 0 0
 
$`1428473_PM_at`
 [1] 0 0 0 0 0 0 0 0 0 0
 
$`1428474_PM_at`
 [1] 0 0 0 0 0

--------

I am not sure what is the proper coding for mm indexes in a case of PM 
arrays. Is there an option in ReadAffy that should be used for PM arrays?
If this can be fixed then rma and justvsn should work.  Thanks.

Roumyana

>> 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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>>
>>     
>
>
>
>   

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