[BioC] Calculating microarray ratios between channels from different arrays

[Naomi Altman]

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
>
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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