Hi,
I've done some updates to the help pages (e.g. ?doCBS), so before
anything I recommend to update to aroma.core 2.9.5 and
aroma.affymetrix 2.9.4:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
On Tue, May 28, 2013 at 9:37 AM, Wei Tang <tangwei1...@gmail.com> wrote:
> Hi aroma.affymetrix developers,
>
> Before I start the analysis, I just want to confirm the CN analysis of 500K
> arrays with doCRMAv2, as I did not find a Vig specific about it.
>
> What I understand is,
>
> 1. run 250K_Nsp
> dsC_Nsp=doCRMAv2(test,cdf="Nsp",verbose=verbose)
>
> 2. run 250_Sty
>
> dsC_Sty=doCRMAv2(test,cdf="Sty",verbose=verbose)
Yes, you can do CRMAv2 preprocessing for each chip type independently.
However, for doCRMAv2() you need to do something like:
dsC_Nsp <- doCRMAv2(dataSet, chipType="Mapping250K_Nsp", verbose=verbose)
dsC_Sty <- doCRMAv2(dataSet, chipType="Mapping250K_Sty", verbose=verbose)
Chip types have formal and strict names, cf.
http://aroma-project.org/definitions/chipTypesAndCDFs
>
> 3. merge them together by "aroma.cn"
Actually, despite its name, you don't need to aroma.cn package here.
The basic CBS methods are still in the aroma.core package. So, after
doing the above doCRMAv2() processing, you then want to do something
like:
tags <- "ACC,-XY,BPN,-XY,AVG,A+B,FLN,-XY"; # Tags added by CRMAv2
res <- doCBS(dataSet, tags=tags, chipTypes=c("Mapping250K_Nsp",
"Mapping250K_Sty"), verbose=verbose);
It's important that the array *names* of the Mapping250K_Nsp and
Mapping250K_Sty pair up, because that is how doCBS() know which array
files to pair up/merge in the segmentation. doCBS() match array
names using the names from getNames(), e.g.
names_Nsp <- getNames(dsC_Nsp);
names_Sty <- getNames(dsC_Sty);
If they don't match up, there are way to "change" the names so they
do, cf. http://aroma-project.org/howtos/setFullNamesTranslator
>
> Would you mind telling me if I am correct with analysis?
>
> I also have SNP5.0 to merge, so should I merge 3 arrays at one time or,
> merge 500K first and then SNP5.0?
You can just include them as a third chiptype set above, e.g.
res <- doCBS(dataSet, tags=tags, chipTypes=c("Mapping250K_Nsp",
"Mapping250K_Sty", "GenomeWideSNP_5"), verbose=verbose);
Hope this helps/get you started
/Henrik
>
> Thank you very much,
>
> Wei
>
> NCI/NIH
>
>
>
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