Hi Henrik ,
Thank you for you suggestion.
but when I ran
res <- doCBS(dataSet, tags=tags, chipTypes=c("Mapping250K_Nsp",
"Mapping250K_Sty"), verbose=verbose);
it complained
"
Error in file(pathname, open = "rb") : invalid 'description' argument
"
do you know how to fix it?
my situation is all paired tumor-normal, 36 paired-samples in SNP5 and
additional 20 paried-samples in 500K
should I use "Multi-source copy-number normalization"
and how about using "doASCRMAv2", does the usage the same as "doCRMAv2" ?;
Many thanks,
Wei
On Thursday, May 30, 2013 6:05:55 PM UTC-4, Henrik Bengtsson wrote:
>
> 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 <tangw...@gmail.com<javascript:>>
> 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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