[BioC] Limma with homemade chip, multiple probes per gene, no replicates?

Gordon [guest] guest at bioconductor.org
Tue Nov 26 14:01:06 CET 2013


I have data from a two-color, homemade, microchip array (one GPR file).
The chip contains multiple probes for each gene (just to be sure I'm using the correct terms: the GPR file has multiple lines with the same NAME and readings of F635 and F532 for each gene of interest). There are also many lines marked with "EMPTY" .

There is only one GPR file, and no replicates at the moment.

(I'm trying to help a friend deal with an existing situation, which is less than ideal - but that's what we've got.)

How do I deal with the multiple probes for each gene?
Should I pre-process the data and calculate the mean/median for each, then feed "limma" only the aggregated values? or is there a better way (taking the variability within each group into account) ?

The data works fine with limma's "read.maimages()", "normalizaeWithinArrays()", and "lmFit()".

However, "eBAyes" and "topTable" do not work (as explained in many other threads, they will not work without replicates).

Despite the fact that it's inadvisable to continue without replicates, is there a way to perform some sort of differential expression analysis?
(Akin to EdgeR's method of working when there are no replicates?)

Many thanks,

 -- output of sessionInfo(): 


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