[BioC] expresso: performing RMA on NON-Affy data?

[J.delasHeras at ed.ac.uk]

Quoting "James W. MacDonald" <jmacdon at med.umich.edu>:

> Hi Jose,
>
> J.delasHeras at ed.ac.uk wrote:
>> Hi Jim,
>>
>> normalisation is not an issue, it's more to do with the   
>> summarisation of probesets and something like 'Expresso' seems like  
>>  a good way to do what I need (and some other things I don't need).
>>
>> I am dealing with Nimblegen arrays. Both two colour (whole genome   
>> promoter arrays, with anything up to 20 probes per probeset), and   
>> one colour "a la Affymetrix" (expression arrays, with anything   
>> between 3 to 8 probes per probeset).
>>
>> I've been dealing with teh two colour stuff just like I used to   
>> deal with my spotted cDNA arrays, using Limma. To summarise the   
>> data... I've used several approaches. Mostly I am not interested in  
>>  the whole 2.7kb that each "promoter region" comprises, so I've   
>> taken subsets blah blah... Anyway, I'm happy with the results there.
>> But for the expression data, I have one channel data, just like   
>> Affy data. Numblegen provides already normalised and summarised   
>> data along with the raw data, and they state they use the RMA   
>> procedure which I've come across with when readingabout Affy chips,  
>>  although I've never analysed Affy data myself.
>>
>> I'm reasonably happy with the data given to me. It looks   
>> reasonable. So I want to be able to do that myself rather than   
>> depending on their data (thus allowing me to do things a bit   
>> differently if I want to), and since the RMA-processed data looks   
>> good, I am interested in finding a way to do RMA myself.
>>
>> You're right, the problem with my trying to make an AffyBatch from   
>> non Affy data is that I'm going to have to create a cdf-like   
>> file... and probably will encounter other obstacles... that's why I  
>>  thought I'd ask here, as there's people who are very familiar with  
>>  that structure...
>>
>> In my naivety, it seems it should be a simple enough task... and as  
>>  I'm using 4 types of arrays mostly... I'd only have to do some  
>> work  to make these work and then just enjoy the ride as new  
>> experiments  roll in...
>> Am I naive? ;-)
>
> Nope. Just looking in the wrong place. If you want to analyze Nimblegen
> single color data, then you need to use the oligo package rather than
> affy.
>
> What package works for which type of oligonucleotide array can be found here:
>
> http://www.bioconductor.org/docs/workflows/oligoarrays/
>
> Best,
>
> Jim

Hi Jim,

thanks for that link.
I now vaguely remember the Oligo package. I tried to use it long ago  
whilst it was still in development but didn't get very far as it  
required some extra files that Nimblegen didn't routinely provide  
(although when scanning the images yourself, with NimbleScan, they can  
be generated easily) and lost interest.
I'll recheck, as it's been a while and things have probably improved a lot.

regards,

Jose

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Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
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