Corina,

Since this is SNP array, probably you should not use P call % in filtering.

Cheng

-----Original Message-----
From: dchip@yahoogroups.com [mailto:dchip@yahoogroups.com] On Behalf Of
Corina Shtir
Sent: Thursday, May 03, 2007 5:51 PM
To: cli@...; dchip@yahoogroups.com
Subject: [dChip] Filtering Genes

Dear Cheng,



I am quite new at running DChipSNP, and have a basic question; when I am
trying to filter genes in preparation of gene clustering analysis (for now
on the NSP 250k Affy chip), I am getting the message “0 of 262264 probe
sets satisfied the filtering criteria: No probe set filtered. You may
uncheck 'Tools/Array list file/Use standardize separator' and retry
Variation across samples: 0.50 < Standard deviation / Mean < 1.50
P call % in the array used >= 20%
The expression level >= 20.00 in >= 20% samples”

Even though I changed the criteria in all sorts of ways, I still got no list
of filtered genes. Could you please help clarify what I am missing?


Note: I chose the option "using all genes, and then the "Mapping250K_Nsp
snp info.txt" for the gene list, and am not clear whether this might have
triggered the problem.

Many thanks.
Corina



~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Corina J. Shtir
Research Associate
University of Southern California
Doheny Eye Institute
1450 San Pablo St.
DEI - 4803
Los Angeles, CA 90033
Office: 323.442.6486
Cellular: 714.337.1052
Email: stir@...





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