Entering edit mode
Ed Schwalbe
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20
@ed-schwalbe-5262
Last seen 10.2 years ago
Dear list,
I have SNP array data run on three platforms: Affymetrix SNP6
(n=~250), Illumina OmniExpress (fresh frozen DNA) (n=12), Illumina
OmniExpress FFPE (n=48).
Since the cancer I work on is comparatively rare, many of our
diagnostic samples are available only as paraffin blocks, so the
arrival of Illumina's OmniExpress arrays which were reported to work
with FFPE material was most welcome (just FYI, 40/48 FFPE arrays have
passed Illumina's own QC procedures available within GenomeStudio).
What I would like to do is to test for recurrent copy number
abnormalities across the three platforms, in a way that minimises
platform-dependent bias as much as possible.
I posted the same question to BioStars and was directed to this paper:
A single-sample method for normalizing and combining full-resolution
copy numbers from multiple platforms, labs and analysis methods
http://bioinformatics.oxfordjournals.org/content/25/7/861.short
However, on investigating this approach, it was clear that this is
geared towards increasing resolution through estimates of CN using
multiple platforms on the same sample, and doesn't consider extending
this to non-repeated samples.
My latest thought is to at least ensure consistent normalisation and
segmentation, firstly by using CRLMM to normalise each platform,
although the metadata for the omni express FFPE platform is not yet
available for me to do this, followed by some form of segmentation
(CBS, GLAD?).
So, after that lengthy introduction, my two questions are:
1) Is there any possibility of releasing a CRLMM metadata file for the
Omni Express FFPE platform?
2) Does anyone have any better ideas of how I might integrate these
data?
Thanks for any guidance you might give!
Best wishes,
Ed
sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.4.4
loaded via a namespace (and not attached):
[1] tools_2.15.0