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! Kanan

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!

That's right Kanan. Unless of course you want to do the analysis completely with probe level data. In which case you may get some pinters in the article "ResurfP: a response surface aided parametric test for identifying differentials in GeneChip based oligonucleotide array experiments" in the deposited research section of Genome Biology: http://genomebiology.com/preprint/. The URL for the full article that partially address this question and of selecting threshold in probe- level analysis of GeneChip arrays (or identification of differentials when studying other features using multiple independent measurements) can be found at http://genomebiology.com/2004/5/11/P14 . Suresh ----- Original Message ----- From: "Matthew Hannah" <hannah@mpimp-golm.mpg.de> To: <bioconductor@stat.math.ethz.ch> Sent: Wednesday, October 06, 2004 9:47 AM Subject: [BioC] P value for each probe > 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! > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Matthew and Suresh, Thank you very much for the pointers. I will be sure to attempt them. Kanan >===== Original Message From Suresh Gopalan <gopalans2@hotmail.com> ===== >That's right Kanan. Unless of course you want to do the analysis completely >with probe level data. In which case you may get some pinters in the >article "ResurfP: a response surface aided parametric test for identifying >differentials in GeneChip based oligonucleotide array experiments" in the >deposited research section of Genome Biology: >http://genomebiology.com/preprint/. The URL for the full article that >partially address this question and of selecting threshold in probe- level >analysis of GeneChip arrays (or identification of differentials when >studying other features using multiple independent measurements) can be >found at http://genomebiology.com/2004/5/11/P14 . > >Suresh > >----- Original Message ----- >From: "Matthew Hannah" <hannah@mpimp-golm.mpg.de> >To: <bioconductor@stat.math.ethz.ch> >Sent: Wednesday, October 06, 2004 9:47 AM >Subject: [BioC] P value for each probe > > >> 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! >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >>