Re: Processing 50+50K chip set? (Was: Re: [aroma.affymetrix])

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Re: Processing 50+50K chip set? (Was: Re: [aroma.affymetrix])

Henrik Bengtsson-4
Hi Yan,

please use an informative subject line of your message and don't
hijack old thread; instead start a new thread/message if the topic is

On Fri, Dec 3, 2010 at 7:59 AM, Yan Jiao <[hidden email]> wrote:
> Hi,
> First of all, I have to say I've got tremendous help from this mailing list, thank you for all of you.
> Then I have to continue asking for help,
> I just realize I probably did something very stupid,
> I was doing DNA copy number segmentation, affymetrix 100k SNP, so as far as I know there are two chips, one chip is obtained by digesting the DNA with Hind, the other chip by Xba.Chip, so in my rawdata folder , I got the .CEL file from both, but in the annotationData folder, sub folder :type, I only got  Mapping50K_Hind240,and .cdf file, .ufl, ugp file for hind.
> My question is, Should I firstly split the .cel file accoding to the chip type and then found the corresponding cdf file etc for Xba.

Yes.  By definition, the aroma framework requires a setup such that
CEL files, just like annotation data files, for different chip types
should be in different subdirectories.  This is for instance
illustrated in the following vignette:

Hope this helps


> Many thanks
> Yan

When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.

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