P call % is 0 for exon array
Cheng Li
Chao,
P call % is 0 for exon arrays, because neither Affy nor dChip computes Presence call for exon arrays.
You can check if there is 3’ to 5’ ratio from Affy software for QC. Or after you do modeling in dChip, array outlier % indicates quality.
Cheng
From: chen chao
[mailto:chen...@gmail.com]
Sent: Wednesday, December 09, 2009
4:02 AM
To: lch...@gmail.com
Subject: Re: dCHIP questions(2)
Hi,Cheng,
This is Chao from U of Chicago. I am sorry to bother you but i have a
question about the dChip software using in the new generation array,
HuGene_st_1.0 array.
I downloaded the dChip built date Jul 13 2009, and set my cel files to data
directory and the download the unsupported CDF file from Affy as the chip
description file.
Also, unzipped the gene info file from this website
http://groups.google.com/group/dchip-software/web/information-file-for-gene-st-arrays?show_cb=1&pli=1
is used as gene info file.
Press OK for the first step calculation. Well, it is weird that when i get the
summary excel file, the percentage of present call are all zero, across
different samples. Then i have no idea how to do the QC, since the golden rule
is P call% larger than 20%.
So my question is that is there any procedure that i missed or i do it in a
wrong way? i can't go further analysis if the QC result like this.
Thanks a lot.
Best,
--
Chen Chao
Psychiatry
University of Chicago