[BioC] probe ID for affymetrix data

[James W. MacDonald]

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).

> 
> 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'.

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.

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.

Best,

Jim



> 
> Thanks!
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826