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On Fri, Dec 3, 2010 at 7:59 AM, Yan Jiao <[hidden email]> wrote:
> 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: