Hello limma people,


I use Limma in the separate channel analysis for two color data, but there
are some small problems :

1) While my differential expression analysis is fine after background
correction ( backgroundCorrect(...) ), when this step is omitted the
following error occur:

Error in intraspotCorrelation(MA2, design) :
  Missing or infinite values found in M or A

So, MA$A,$G include NA values, but I don't understand why they appear and
how to dill with them, to avoid this error. My raw data doesn't include NA
values.


2) I need to moralized intensities of my microarray results, so it can be
exported for other programs. Is the following formula a correct way to
extract log intensities from MA data ?

logR <- MA2$A + (0.5*MA2$M) # red = Cy5
logG <- MA2$A - (0.5*MA2$M) # green = Cy3


Thanks for your previous help,
Assaf

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