[BioC] Inconsistency in RMA results from 'affy' and results from 'oligo'

[Steve Lianoglou]

On Aug 10, 2009, at 11:24 PM, Peng Yu wrote:

> On Mon, Aug 10, 2009 at 9:53 PM, Steve
> Lianoglou<mailinglist.honeypot at gmail.com> wrote:
[snip]

>> What is a probe set? How is it different from a gene? Since you  
>> have many
>> more probeset level numbers than gene/transcript numbers, does that  
>> mean
>> there are more than 1 probeset to a gene? Is that what this is  
>> saying here?
>> http://www.affymetrix.com/support/help/faqs/mouse_430/faq_8.jsp
>
> The above webpage says "Probes in a gene family probe set (_a set) all
> cross-hybridize to the same set of
> sequences that belong to the same gene family (i.e. having same name  
> in the
> "geneCluster" column)." But I don't understand what the word
> "sequence" means in this context?

Look further below: does the diagram make it any more clear? When the  
text says that the probes are (cross-)hybridizing to *some* sequence,  
the sequence being referred to is the input cDNA from your sample that  
you are testing on your microarray.

> Does it mean a transcript?

The text is explaining different ways of how a probe might hybridize  
uniquely (or not) to something in the genome that's under test.  
Unfortunately not every probe on a microarray hybridizes to exactly  
one place in the genome, so there is some ambiguity that arises in  
your signal that you should understand/appreciate.

>> Or this figure (and the rest of the publication), here?:
>> http://www.biomedcentral.com/1471-2105/8/108/figure/F1
>>
>> Has someone asked something like this on this mailing list before?
>> https://stat.ethz.ch/pipermail/bioconductor/2009-January/025791.html
>
> This thread does not provide very useful information.

Are you sure?

The poster is asking how to get probe level data (what you are getting  
from the oligo package) from using rma in the affy package. There's  
even code in a separate message in that thread:

https://stat.ethz.ch/pipermail/bioconductor/attachments/20090112/cc275d96/attachment.pl

See where it says "If you need normalized but unsummarized probe level  
intensities ..." and the code that follows? If you use something  
similar to the code there, will the affy "rma" recapitulate something  
more like what you're seeing the oligo::rma? (I don't know, just  
asking).

>> In the meantime, I see that Sean has provided you a direct answer,  
>> so kudos,
>> but I'd just suggest taking a bit more of this work on yourself. I  
>> think it
>> will help to make more sense of the answers you will inevitably get  
>> on this
>> list.
>
> What does "kudos" mean?

Sorry, it's a bit of an english colloquialism that means something  
like "congratulations"

http://dictionary.reference.com/browse/kudos

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
  | Memorial Sloan-Kettering Cancer Center
  | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact