[BioC] Kooperberg introduces Nas??

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Fri Jun 4 15:39:33 CEST 2004


I have read in some data using the limma examples and everything is
fine, I have used the kooperberg algorithm and everything works, APART
from one single spot where I have an NA for some reason:

> RGmodel$R[2483,]
[1] 255 919 371 315
> RGmodel$G[2483,]
[1] 152 929 116  NA

Now, the spot in question has a Cy3 foreground mean of 2256 and a Cy3
background median of 4782.

OK, so it is a bad spot.  But GenePix hasn't flagged it, perhaps because
background is only high in the Cy3 channel - whatever.

Anyway, I didn't realise that Kooperberg could introduce NAs into the
data set - I thought it was this type of problem that kooperberg was
meant to address? (ie negative spots).

Thanks in advance for your help


More information about the Bioconductor mailing list