Hi Elai/Zaid.
You'll want to be careful with all this (i.e. linear models on
unnormalized data ... or maybe you are standardizing some other way),
but yes you can run the probe level model fits on any AffymetrixCelSet
object.
The standard RMA procedure would BG adjust, then quantile
Hi Yu Chuan.
I'm still mystified by this. Can you check that the PLM was
successfully fit? Pull out some chip effects, maybe.
Cheers,
Mark
On 25-Nov-09, at 4:51 AM, Yu Chuan wrote:
Mark,
I think the below info. may help too. Looks like all the gene-level
NUSE are 0. How could this
