[BioC] Bioconductor package to map probe set ids from one chip to another chip

Hattem, Gaye GLH at stowers.org
Fri Apr 24 21:21:18 CEST 2009


Although it's not in a Bioconductor package this mapping is provided in a series of text files from Affymetrix http://www.affymetrix.com/support/technical/comparison_spreadsheets.affx. For each pair of platforms compared you will find 3 files: best match, good match and complex. The spreadsheets compare probe sets using alignment of the representative sequences, alignment of PM probes to probe selection region, and alignment of PM probes to representative sequence. A detailed explanation is available in the user guide. I would also agree with Marc's comment that you need to be very careful that you understand what this mapping actually means.

Gaye

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Marc Carlson
Sent: Friday, April 24, 2009 12:11 PM
To: Marc Carlson
Cc: Andrew Yee; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Bioconductor package to map probe set ids from one chip to another chip

One more thing,

I feel that I have to add an additional comment here.  And that is to PLEASE be careful (with whatever it is that you have planned).  In many cases the probesets in question may have been made to measure a completely different transcript on one platform than on another.  So while we can definitely join them via their association with a particular gene in the way that I have shown you here, you could end up interpreting things very badly if you don't pay very careful attention to what they are actually meant to be sticking to.

  Marc



Marc Carlson wrote:
> Hi Andrew,
>
> I am really unsure about why you would want to do this, but if you 
> did, you could grab the annotation packages for those two platforms 
> and do something like this:
>
> library(hgu95av2.db)
> library(hgu133a.db)
>
> ##just to grab some real probesets for our example keys = 
> Lkeys(hgu95av2ENTREZID)[100:200]
>
> ##now lets map 'em
> ##1st step is to get the entrez gene ID (which all of the human 
> packages use as a central ID) EGs = mget(as.character(keys), 
> hgu95av2ENTREZID, ifnotfound = NA)
>
> ##Then use the other package to the probes that go with those entrez 
> gene IDs otherProbes = mget(as.character(EGs), 
> revmap(hgu133aENTREZID), ifnotfound = NA)
>
> For this example I have assumed that you are trying to map between 
> platforms of the same species.  For different species that problem 
> becomes a lot more challenging.
>
>
>   Marc
>
>
>
>
> Andrew Yee wrote:
>   
>> This is a naive question, but is there a Bioconductor package that 
>> will map probe set ids from one chip to another chip?
>> Thanks,
>> Andrew
>>
>> 	[[alternative HTML version deleted]]
>>
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