Hi.
On Thu, Jan 13, 2011 at 8:56 PM, Zhu, Lihua (Julie)
<julie....@umassmed.edu> wrote:
> Henrik,
>
> Thanks so much for developing such a useful package!
>
> I have followed the instructions on http://www.aroma-project.org/.
>
> A list of copy numbers for all samples and units were generated. Now I want
> to annotate the copy number estimate C with SNPs and gene names. Could you
> please shed some light on how to proceed?
>
> theta.ALL.BCR.ABL <- do.call(cbind, lapply(1:length(cesN$Names),
> function(i){
> ce <- getFile(cesN, i)
> theta <- extractTheta(ce)
> }
> ))
Instead of doing the above, just do:
theta.ALL.BCR.ABL <- extractTheta(cesN, drop=TRUE);
(assuming that you are doing total CN analysis, i.e. combineAlleles=TRUE.)
> ceR <- getAverageFile(cesN.r, verbose=verbose)
> thetaR <- extractTheta(ceR)
> thetaR = as.vector(thetaR)
Instead, just do:
thetaR <- extractTheta(ceR, drop=TRUE);
> C <- 2*theta.ALL.BCR.ABL/thetaR
To add the CDF unit names as rownames, just do:
unf <- getUnitNamesFile(cesN); # This will for Affymetrix be the CDF
rownames(C) <- getUnitNames(unf);
which gives:
print(C[2001:2003,1:4]);
GSM226867 GSM226868 GSM226869 GSM226870
SNP_A-1512786 2.009220 2.438844 1.889013 1.782385
SNP_A-1512840 1.149404 1.741206 1.759043 2.096061
SNP_A-1513972 2.038601 2.077377 1.623648 1.530445
Hope this helps
/Henrik
>
> Thanks so much for your kind help!
>
> Best regards,
>
> Julie
>
>
>
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