[BioC] normalize.AffyBatch.quantiles and NA values

[odlc at uchicago.edu]

Hello,

I am trying to understand how normalize.AffyBatch.quantiles
works. From what I understand of the code, it seems that
rows (corresponding to a probe) which contain even a single
NA are dropped; then, the quantile-normalization method 
described in Botstein et al. is applied to the remaining rows,
and these normalized rows are put back into the original
batch. 

In other words, values in a row that contains NA's
remain unchanged.

Questions:

- Is this really how it works?

- If yes, is this the intended behavior?

Thank you,

Omar.