[BioC] [Bioc] Removing outlier/masked probes and gcRMA

[Amy Mikhail]

Hi Andrew,

Just thought I'd refer you to a discussion on the list a few weeks ago
about removal of probesets, which might help.

As I understand it, the problem is that you need to remove your probes (or
probesets) from the cdf as well as your affybatch object, so that they
match.    There is a chunk of code written by Ariel Chernomoretz and
modified by Jenny Drnevich which does exactly this.  You can find it here:

http://article.gmane.org/gmane.science.biology.informatics.conductor/9869/match=remove+probes+cdf

See also below for a thread to the discussion:

http://search.gmane.org/?query=Amy+Mikhail+genefilter+questions&author=&group=gmane.science.biology.informatics.conductor&sort=relevance&DEFAULTOP=and&%5B=2&xP=amy%09mikhail%09genefilter%09questions&xFILTERS=Gscience.biology.informatics.conductor---A

It's quite versatile as you can apply the code and remove your probes
either before anything or after background correction, for example (what
stage is best would depend on what your set of removed probes does to the
variance and standard  errors, etc as Jim mentioned).

Hope this helps,
Amy

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Thanks, Jim, for the thoughts below.  Unfortunately, we are using a
custom Affy chip design here, so those precomputed ones won't work for
us.  But we could certainly create a custom CDF file for our chip type
too...

... but it surprises me somewhat that there isn't an alternate solution.
First, what do people do with an AffyBatch object which was read in
using the rm.mask option if it can't be used for further analyses?  (Or
is this a failing in how gcrma specifically deals with NAs?)  And
second, although custom CDFs would be great for dealing with
ChipType-specific effects (e.g., SNPs), how do people deal with
chip-specific effects (e.g., scratches and debris)?  Just a couple of
thoughts...  Any additional ideas are welcome, but we'll be pushing
ahead on custom CDFs in the mean time...

Cheers,
-andrew




-------------------------------------------
Amy Mikhail
Research student
University of Aberdeen
Zoology Building
Tillydrone Avenue
Aberdeen AB24 2TZ
Scotland
Email: a.mikhail at abdn.ac.uk
Phone: 00-44-1224-272880 (lab)
       00-44-1224-273256 (office)