Question: request for simple usage of probe level normalisations
12.0 years ago by
Ido M. Tamir • 320
Ido M. Tamir • 320 wrote:
Dear All, a) I don't know, if sequence based models like GCRMA, which I read stands actually for "GeneChip (tm)" not GC content, can be extended to other platforms. I am just looking at single color agilent chips and there is a gc content bias: log2(intensity)~gc percentage: Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 1.023391 0.105189 9.729 <2e-16 *** gcp 0.121826 0.002503 48.666 <2e-16 *** b) I know one should not request/ask open source deveoplers for something but: if GCRMA is applicable to other platforms, then it would be nice if it could be used in a simple way with these other platforms, and new platforms for oligo chips are getting more and more common. I read the information from the oligo package and of the makePDpackage which seems to be superseeded in the future by the pdInfoBuilder. Would it be possible to make this simpler somehow? I don't know exactly what information is actually needed by the downstream analysis with GCRMA, but wouldn't it be sufficient that for the creation of a new environment I would need just 2 simple tab delimited text files*. Then one could simply make a script that converts ones own format (which are not .ndf or .cdf) to this _simple_ tab delimited format whose specification is clearly outlined in the package vignette. Maybe I am underestimating the complexity (ignoring spatial information on chip) or its already there (yes, cdf etc.. files can be faked). thank you very much, ido *eg.: file1: oligo name, sequence, gene name (for grouping multiple oligos) file2: annotation gene or oligo name (if not grouped), annotations....
ADD COMMENT • link •