[BioC] Background corrected PM, MM intensities

[James W. MacDonald]

Rad Nag wrote:
> Hello:
> 
> I am currently trying to understand the effect of background
> subtraction on gene expression in affymetrx genechip arrays. It will
> be really helpful if someone could let me know
> 
> "How to extract the PM and MM intensities along with their
> locations/coordinates on the chip after background correction?"
> 
> I am enclosing a part of the code (my first try):
> 
> library(affy) Data <- ReadAffy("File1.CEL") %then I load the
> corresponding CDF files eset <- mas5(Data, normalize = FALSE);
> 
> Now I have the background corrected values in "eset". 

No, you have the unnormalized MAS5 expression values in eset, so there 
are no longer PM and MM intensities. If you just want background 
corrected values you have to do something like this:

abatch <- bg.correct.mas(Data)

Then you can get the intensities and coordinates using some combination 
of pm(), mm() and indexProbes().

See e.g. ?indexProbes for more information.

Best,

Jim


How can I get
> the PM and MM intensities along with their coordinates from eset.
> 
> Thanks
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623