Hello,
Thanks for aroma.affymetrix and this helpful site.
I was hoping to get some general advice. I know CRMAv2 is a single
array method and thus makes processing different arrays in parallel
possible.
I was wondering how you would setup the rawData and annotationData
directories when doing multi-staged analysis.
For instance, for my project I have 20 patients. I will be getting
the data for the first 10 patients immediately, and then the data from
the remaining 10 patients a few weeks later. All experiments will be
performed on the same chipType.
I was thinking on this structure:
--rawData/
--patient01/GenomeWideSNP_6
--patient02/GenomeWideSNP_6/
--patient03/GenomeWideSNP_6/
...
--patient20/GenomeWideSNP_6/
And then preprocessing each patient separately in an R session with:
dataSet <- "patient01";
chipType <- "GenomeWideSNP_6";
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full");
dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE,
verbose=verbose);
Once I get all the arrays and have preprocessed them I would like to
segment the data using CBS. The first 10 patients are normal and the
last 10 diseased -- i.e. a tumor-normal arrays for each sample.
However, since I processed each array individually each would have
their own AromaUnitTotalCnBinarySet. Would I just read each in
individually, and then manipulate it in order to create the necessary
matching of normal over tumor needed for the CBS algorithm?
If down the road we get another 20 arrays again with tumor normal
samples how would I integrate these new arrays with my previous
arrays? Just create additional directories:
--rawData/
--patient21/GenomeWideSNP_6
--patient22/GenomeWideSNP_6/
--patient23/GenomeWideSNP_6/
...
--patient40/GenomeWideSNP_6/
I hope I explained my question reasonably clear.
Thanks, Greg
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