Question: How to get probe names for raw intensity values?
0
gravatar for vleblanc
3.1 years ago by
vleblanc0
Canada
vleblanc0 wrote:

I'm trying to get raw intensity values for a particular probeset from the Affy HuGene 2.0 array. I've tried getProbeInfo:

> subset(getProbeInfo(raw, target = 'probeset'), man_fsetid == "16862673")
           fid man_fsetid
378679  956480   16862673
450843 1140178   16862673
560361 1420274   16862673
602825 1535007   16862673

Is 'fid' equivalent to the rownames of the intensity matrix (exprs(raw))? The number of rows are not equivalent so I hesitate to assume this.

Thanks in advance for any help.

oligo • 439 views
ADD COMMENTlink modified 3.1 years ago by James W. MacDonald52k • written 3.1 years ago by vleblanc0
Answer: How to get probe names for raw intensity values?
0
gravatar for Eleni Christodoulou
3.1 years ago by
Singapore
Eleni Christodoulou150 wrote:

Hello,

I am not working with Affy Arrays but with Illumina. I guess the same things exist for both cases, though. For illumina, there is a manifest file for each array, which maps the  rownames of the array to symbols, entrez_ids etc. One of the manifest's columns is called 'array_address_id'. This is a big integer, similar to the fid number you described above. Could you find the manifest  for your case?

 

ADD COMMENTlink written 3.1 years ago by Eleni Christodoulou150

Illumina and Affy arrays are completely different. There is no manifest file for Affy arrays.

ADD REPLYlink written 3.1 years ago by James W. MacDonald52k
Answer: How to get probe names for raw intensity values?
0
gravatar for James W. MacDonald
3.1 years ago by
United States
James W. MacDonald52k wrote:

The fid IS equivalent to the row of the matrix you get from accessing the exprs slot from your GeneFeatureSet. So you could do

> z <- getProbeInfo(dat, target = "probeset")
> zlst <- split(z[,1], z[,2])
> zlst["16862873"]
$`16862873`
[1]  855406 1605173 1878834
ADD COMMENTlink written 3.1 years ago by James W. MacDonald52k

Great, thanks for your help!

ADD REPLYlink written 3.1 years ago by vleblanc0
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