SNP 6.0 reference genotype file & conversion script
Cheng Li
I got the zip file and put it at
http://www.dchip.org/hapmap_sam.zip
http://www.dchip.org/genotype_converter.py
Your message below should help to explain its usage, but feel free to
reply to the group email if you would like to add more.
Thank you very much.
Cheng
From: Sam Volchenboum [mailto:s...@volchenboum.com]
Sent: Wednesday, December 16, 2009 6:18 PM
To: Cheng Li
Subject: Re: reference genotype file conversion script
Cheng, I've attached the latest version of my conversion script.
I hope it helps someone. Would you rather I just post it to the google
groups?
I will compress the final genotype file and put it somewhere for you
to access.
Thanks.
sam
>> Cheng,
>>
>> I'm attaching a short Python script I wrote that converts a SNP 6.0
affy
>> results file into a file that can be used for "Reference genotype
file."
>> Maybe someone will find it useful. It only takes a few minutes to
run, vs.
>> using dChip which can take much longer to generate the file.
>>
>> Also, if you want, I can make the SNP 6.0 reference genotype file I
made
>> available, though I probably can't host it (it is about 900 megs).
>>
>> If you want, I could customize / generalize the program to convert
other
>> types of files - I just need to know which ones are needed and for
someone
>> to send me the header and a few rows of the file.
>>
>> -sam
>>
Renzoni, Elizabeth
I wonder if I could ask your help for what is probably a very simple issue. Across chips, I would like to find all the genes that have a similar expression pattern to one gene selected within a clustering page. The online manual suggests going to "Clustering", and then clicking on "similar profile", but under the clustering tab I cannot find this command, nor can I find it elsewhere. Is there a something very basic that I am missing?
Thank you for your help
Elizabeth
Cheng Li
Please use the "Analysis/ANOVA & Correlation" function:
http://biosun1.harvard.edu/complab/dchip/timecourse.htm#corr_filter
Cheng