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
Dear group,
I am new to microarrays and bioinformatics field and
I am reposting my queries anticipating that some one
might help me. Please excuse me.
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