[BioC] miRNA normalisation

[James W. MacDonald]

Hi Dermot,

On 1/23/2012 9:10 AM, Dermot Morris wrote:
> Dear all,
>
>
>
> I would like to  extract the probesets corresponding to a single species
> ("bta")  from an Affymetrix
>
> miRNA array  to examine the effects of normalisation using a single
> species compared to using all probes on array.
>
>
>
> Is there a simple way to subset an affybatch at the probe level prior to
> normalisation ?

No. You can subset an AffyBatch at the chip level (essentially 
subsetting by column), but subsetting by row has been deprecated for 
years now.

Hypothetically you could go through the AffyBatch and remove all non-bta 
probes by hand. You then might have to do something to the cdf package 
as well. I'm not sure without doing a close examination of the code.

You could also hypothetically use the pm() function with LISTRUE = TRUE, 
to extract all the probesets into a named list, then normalize all the 
bta probes separately. You could then put the normalized bta probes back 
into that list, convert to a matrix that is correctly ordered (see 
showMethods(pm, class = "AffyBatch", includeDefs = TRUE)), and then use 
the pm() function to put it back into the AffyBatch.

An alternative of this would be to extract as a list, then collect the 
row.names() of all the probesets that are bta probes. You could then 
re-extract using pm() without the LISTRUE argument, and use the 
row.names you extracted to remove those rows, normalize the data, and 
then put back into the original matrix. You could then use pm() to stick 
the data back into the AffyBatch and go from there.

You could also hypothetically do the bg.correct() step on your 
AffyBatch, then extract the pm values into a list as above, then do the 
normalization and summarization step by hand on the list (the 
summarization step of rma() can be emulated using the medpolish() function).

None of those possibilities is simple, however.

Best,

Jim


>
>
>
> Best Regards,
>
>
>
> Dermot
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

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