Calculating microarray ratios between channels from different arrays
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Naomi Altman ★ 6.0k
@naomi-altman-380
Last seen 3.9 years ago
United States
Until proven otherwise, I think that a channel by channel analysis in which array is entered (preferably as a random effect) along with dye is valid. I.e. I treat the entire design as an ANOVA and look at any contrast that is reasonable. --Naomi At 03:09 PM 9/14/2004 +0100, michael watson (IAH-C) wrote: >Hi > >I wondered what the list felt about calculating ratios between channels >from separate microarrays? > >Let me explain. I have come across an experiment (not designed by >myself) where I have the following: > >+ve cell lines - cell lines with random genomic insertions that display >a +ve phenotype >-ve cell lines - cell lines with random genomic insertions that display >a -ve phenotype >Parental cell lines with no genomic insertion > >Now to me it would have made sense to compare +ve vs parental and -ve vs >parental to find those genes which are present in the insertions but not >in the parent which may be contributing to the phenotype. > >However, the experimenter did not do this; they compared each +ve cell >line to the -ve cell lines, and also the parental cell lines to the -ve >cell lines. > >So intuitively what I want to do is calculate ratios of +ve/parental and >-ve/parental for each of the experiments, when what I have is +ve/-ve >and parental/-ve. > >Is it valid simply to take the (single) list of values for the parental >cell line and use that repeatedly as the denominator for the +ve and -ve >channels from the other arrays? > >Thanks >Mick > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111
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