[BioC] P value for each probe

[Matthew Hannah]

Kanan,

I think you are possibly getting confused. There is no such thing as a
p-value for each probe. Maybe you are thinking of the mas5
present/absent call p-values which can be obtained for each probeset. In
which case you want this function from the affy package -
mas5calls(Data)

If you want to find out more about pm, mm, probesets etc... try calling
the html help from R using
help.start()
and browsing the help for the affy package, also perhaps try some of
these
http://www.bioconductor.org/labmat.html

Some of the affymetrix literature from their website also explains what
stats mas5 uses.

Also a minor point 
eset <- rma(Data)
is redundant in your example below. pm is extracted from Data, not eset.

HTH,
Matt


#####


Bioconductor users,


I have four CEL files from Affymetrix Mouse Array 430_2 and am trying to
get 
the p values per probe. I would like to write this out into a tab
delimited 
text file. Where am I stalling? This is what I've done:


Change dir(to where CEL files are saved)
Data <- ReadAffy()
eset <- rma(Data)
my.pm.data <- pm(Data)
write.table (my.pm.data, file = "pmprobes3.csv", sep = ",", col.names =
TRUE, 
row.names = probeNames(Data))

This result is the following:

Probe Sam1 Sam2 Sam3 Sam4
1415670_at01 340 383 376 320
1415670_at02 794 932 734 697
1415670_at03 1117 1366 1013 932
1415670_at04 97 97 148 94
1415670_at05 387 405 367 402
1415670_at06 485 553 391 343
1415670_at07 458 509 410 385
1415670_at08 507 684 616 545
1415670_at09 311 392 576 463
1415670_at10 691 822 688 588
1415670_at11 512 726 3201 2317
1415671_at01 1230 1212 873 770
1415671_at02 886 877 794 729
1415671_at03 1472 1682 1263 1152
1415671_at04 1171 1214 948 914
1415671_at05 390 479 435 396
1415671_at06 462 513 423 389
1415671_at07 987 1151 1102 815
1415671_at08 992 1066 1203 1013
1415671_at09 489 534 501 385
1415671_at10 401 509 379 293
1415671_at11 1443 1686 1410 1215

Each gene has 11 pm probes.
How can I get the p-value for each probe?

Please help me out and thanks in advanced!