[BioC] normalisation for universal reference in 2 channel arrays
pwilkinson at videotron.ca
Wed Jul 28 22:02:49 CEST 2004
I would like to know some alternative to normalization for 2 channel
experiments against universal, where samples may have been hybridized in
seperate batches where the universal RNA has changed lot (should not have
happened but it did). What is the same between the batches is that what
looks like up-regulated compared to the universal iis upr-egulated, and
what is down-regulated looks down-regulated. The difference is that the
down-regulated (and not in the up), so so much more down-regulated in one
of the batches. It looks like to be that the universal has more mRNA
abundance in one batch over the other.
I have samples that can be divided into 2 classes: 0,1, and within each
class I have samples that have been run at different times. I would like to
treat my universal channel uniformly across all samples (assuming that my
universal changed lot), and then adjust the Sample (Red) channel to that.
is the normalizeBetweenArrays with the method="Gquantile" option the right
option for this?
What is the complete work-flow for this case? And after I have normalized
within the Arrays, can I go on to scale option for normalizing between arrays.
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