Hi.
On Wed, Jun 5, 2013 at 11:31 AM, Wei Tang <tangwei1...@gmail.com> wrote:
> 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?
1. What does traceback() output immediately after you get that error?
2. Can you show me your complete script?
3. What is your sessionInfo()?
>
> 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"
Possibly - depending on the amount of attenuation in the different
chip type hybridizations (depends on date, lab etc) you may see a
small improvement in power to detect change points. However, even
without doing MSCN it is still always better to merge platforms (as
doCBS() does) than running only single chips, cf. Figure 6 in H.
Bengtsson, A. Ray, P. Spellman & T.P. Speed, A single-sample method
for normalizing and combining full-resolution copy numbers from
multiple platforms, labs and analysis methods, Bioinformatics 2009
[http://aroma-project.org/publications].
> and how about using "doASCRMAv2", does the usage the same as "doCRMAv2" ?;
That's if you plan to infer parent-specific CNs. If you don't know
yet, use doASCRMAv2(). Everything should work the same with doCBS().
/Henrik
>
> 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> 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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>
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> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
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> traceback(), and 3) to post a complete code example.
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