[BioC] (no subject)

James W. MacDonald jmacdon at med.umich.edu
Tue Nov 30 20:53:03 CET 2004

hrishikesh deshmukh wrote:
> Hello All,
> I have a bunch of .CEL files, i want to filter
> intensity values:
>>1) PM, MM has to be between 200 to 20000 units.
>>2) PM can be < 200, MM should be <= 20000 units.
>>3) MM can be < 200, PM should be <= 20000 units.

Well, I guess the third time is a charm ;-D.

I think the main reason you have yet to get a response is that your 
question is not very clear. Do you simply want to filter the PM and MM 
values and output them? Do you want to only use those PM/MM pairs that 
fulfill these criteria to compute expression values? Conversely, if you 
only want to compute expression values for genes whose PM/MM values 
fulfill these criteria, could you do the filtering after computing 
expression values?

If, for a given probe the PM value is outside one of these bounds do you 
want to filter out only that one PM value, or the corresponding PM 
values for all the other chips as well?

Depending on your answers to these questions, this can be a simple thing 
or quite difficult.

Have you read 'An Introduction to R'? This covers subsetting, and should 
get you well on your way to doing something. However, since it is not 
clear what you want, this may not be sophisticated enough.

>>How do i apply these conditions to 17 .CEL files?!
> then write the result to a file (.txt/.xls).
>>How do i extract sequence information for the list
> which i get from the above step.
> Thanks,
> Hrishi
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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

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