[BioC] Affymetrix file with probe set id

Srinivas Iyyer srini_iyyer_bio at yahoo.com
Sun Oct 3 18:19:40 CEST 2004


Dear group, 
I am trying to process some affymetrix CEL files to a
format that my programs can understand.
For that I need to let my program know the intensity
readings(mean and stdv) by name of 
probe set instead of X,Y coordinates. 
Using R, can I get a file that will have an extra
column of probe set IDs in addition to 
spot coordinates. Is there a method(steps of commands)
to get a file with all spots along 
with affy probeset.

Can I get a output that has an extra column like the
following:
[INTENSITY]
NumberCells=409600
CellHeader=X    Y       MEAN    STDV    NPIXELS
1000_at	0       0     384.0   37.3     25
1001_at	1       0     11930.3 907.7    20

Also, is this spot coordinates 0, 0 is always fixed
for a prticular chip (Logically speaking
it should not change). however, I would like to know
more information about this.

Thank you. 
Srini Iyyer



More information about the Bioconductor mailing list