[BioC] subsetting an eset object with a defined list

[Celine Carret]

Thanks Sean,
unfortunately, it doesn't work, it says 

> exprs(eset)[as.character(list[,1]),]
Error: subscript out of bounds

as for the affy Ids, it's fine because those IDs replace the affy ID in our custom array, so these are present in the eset as stated.

any other idea?
best wishes,
Celine




>exprs(eset)[as.character(list[,1]),]
>
>  
>
>>[1] NA   NA   NA   NA   ....
>>...
>>[901] NA   NA   NA   NA
>>
>> >dim(list)
>>
>>[1] 904 1
>>
>> > exprs(eset)[as.character(list)]
>>
>>[1] NA   NA   NA   NA   ....
>>...
>>[901] NA   NA   NA   NA
>>
>> >head(list)
>>
>>    V1
>>1 "PF11_0211"
>>2 "PF14_0749"
>>3 "PF10_0015"
>>4 "PFB0695c"
>>5 "PF14_0316"
>>6 "PF11_0039"
>>    
>>
>
>These are not affy IDs, are they?  If not, you will need to map these gene 
>names back to affy IDs before you can use them for subsetting.
>
>It is probably worthwhile reading a bit of the Intro to R manual and, if you 
>don't have it, consider getting a copy of the Bioconductor book.
>
>Sean
>
>  
>

-- 
----------------------------------------------------
Celine Carret PhD
Pathogen Microarrays group
The Wellcome Trust Sanger Institute
Hinxton, Cambridge CB10 1SA, UK.
tel. +44 (0)1223 494 940
fax. +44 (0)1223 494 919
email: ckc at sanger.ac.uk
http://www.sanger.ac.uk/PostGenomics/PathogenArrays/