Hi everyone,

Sorry if this is a basic question, but I knew this was the group who could
help me out.  My question concerns the pm() function in R/affy.  When you
call this function for a specific probeset ID (example: pm(CELData,
genenames = c("1427760_s_at")) the PM signal values for each probe in the
given probe set are returned in an output like this:

1427760_s_at1                              1394
1427760_s_at2                               382
1427760_s_at3                               128
1427760_s_at4                               106
1427760_s_at5                               231
1427760_s_at6                               516
1427760_s_at7                               138
1427760_s_at8                               215
1427760_s_at9                               369
1427760_s_at10                              991
1427760_s_at11                              530

In this case, there are 11 values returned (Mouse 430v2.0) with a suffix for
each probe ascending from 1-11.  My question is this: Does that order
correspond to 5' - 3' ordering of the probes in the probeset against the
transcript, similar to what is on the NetAffx website and in the
tab-delimited text file of probes available from Affymetrix?

Thanks very much for your help,
Jason

Jason Affourtit
Senior Manager, Phenotyping Sciences
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609

	[[alternative HTML version deleted]]

