[BioC] probe ID for affymetrix data

Xingmei Wang xwang5 at mail.med.upenn.edu
Mon Mar 30 17:51:59 CEST 2009

Thank you Jim for kindly answering my questions! Very much appreciated!!

James W. MacDonald wrote:
> Hi Xingmei Wang,
> Xingmei Wang wrote:
>> Hi all,
>> I have problems analyzing affymetrix data and would like to seek help 
>> from the list.
>> 1. I tried to create the design file by copying the design table from 
>> abf1 data. In Windows version R2.8.0, the data name is "abf1", while 
>> in Unix R2.8.0, the data name is "abf1.raw". Why?
> I assume because you named it that way. R doesn't append different 
> things to variable names randomly (or based on the OS).
*I didn't name abf1 data. It's a data coming with package "maanova". I 
assumed people on this list have experience using this data. :-P *
>> 2. I saw probeID for abf1 data has the following format: 
>> "1415670_at"   "1415671_at"   "1415672_at"   "1415673_at"   
>> "1415674_a_at". But the probe IDs I obtained from my data look like 
>> this:
>> "7892501" "7892502" "7892503" "7892504" "7892505" "7892506" "7892507"
>>  "7892508" "7892509" "7892510"
>> Is there something wrong with my data?
> Well, the probe IDs for abf1 appear to come from the Mouse430_2 chip, 
> and your data appear to be from either a Human Exon ST or Gene ST 
> chip. So it depends on what exactly you mean by 'wrong'.
*Thanks for this answer! My data did come from a Human Exon ST chip*
> I think you need to think a bit more about what you are doing and what 
> you expect, and perhaps then you will be able to formulate a question 
> that can be answered by someone on this list. Right now it isn't clear 
> to me what you have done, nor is it clear what you expect, so it is 
> impossible to help clear up any misunderstanding you may be having.
*Sorry if I didn't make my questions clear! I indeed don't have much 
experience on genetics data, so it's hard to formulate a question. I'll 
try to do more research on the archives next time.*
> Also, please read the posting guide:
> http://www.bioconductor.org/docs/postingGuide.html
> Asking the right question in a reasonable manner is not that 
> difficult, but it does take some work on your part, and the likelihood 
> of getting answered is often directly proportional to how well you ask 
> the question in the first place.
*Totally agree!!*
> Best,
> Jim
>> Thanks!
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: 
>> http://news.gmane.org/gmane.science.biology.informatics.conductor

Xingmei wang , MS

Biostatistics Analysis Center (BAC)
University of Pennsylvania School of Medicine
Center for Clinical Epidemiology and Biostatistics
519  Blockley Hall
423 Guardian Drive
Philadelphia, PA 19104

Phone: 215-898-1560
Fax:   215-573-1203
Email: xwang5 at mail.med.upenn.edu
Website:  http://www.cceb.med.upenn.edu/services/bac/

More information about the Bioconductor mailing list