Hi, I think I have serious problems with expresso() I use option rm.mask=TRUE in ReadAffy() and then tried to use expresso (daten, bgcorrect.method="rma",normalize.method="quantiles", pmcorrect.method="pmonly",summary.method="medianpolish") and several other settings. as stated yesterday I get thousands of Error messages and only NAs as an output (for ALL probesets) when I have masked just 2 oligos one from probe set 1000_at and one from probe set 1001_at. e.g. MASKED part in my CEL-files look like [MASKS] NumberCells=2 CellHeader=X Y 399 560 399 561 on the other hand it seems to make no difference on the expression value of probe set 1000_at whether I mask zero, one or all 16 oligos, the expression value of 1000_at is always the same. the MASKED part in my CEL-files looks for "all 1000_at oligos masked" like this: [MASKS] NumberCells=16 CellHeader=X Y 399 560 544 186 530 506 617 350 459 490 408 546 484 312 548 334 578 370 498 466 503 442 482 440 397 546 352 466 253 496 228 632 has anyone countered the sample problem? since it seems to be same with outliers: how do bioconductor users handle OUTLIERS and MASKED oligos? or am I completely wrong with what I intend to do? gunter

What you are seeing is a reflection of the fact that some preprocessing/summarization functions do not handle missing values well or at all (masked cells are treated as missing values). Typically for RMA expression measures (which seems to what you are aiming for) we do not use masks instead allowing the robustness of the summarization procedure deal with problem probes. Ben On Wed, 2003-10-29 at 07:22, weiss wrote: > Hi, > > I think I have serious problems with expresso() > > I use option rm.mask=TRUE in ReadAffy() > and then tried to use > expresso (daten, bgcorrect.method="rma",normalize.method="quantiles", > pmcorrect.method="pmonly",summary.method="medianpolish") > and several other settings. > > as stated yesterday I get thousands of Error messages > and only NAs as an output (for ALL probesets) > when I have masked just 2 oligos one from probe set 1000_at > and one from probe set 1001_at. > > e.g. > MASKED part in my CEL-files look like > [MASKS] > NumberCells=2 > CellHeader=X Y > 399 560 > 399 561 > > > on the other hand it seems to make no difference on the expression value > of probe set 1000_at whether I mask zero, one or all 16 oligos, > the expression value of 1000_at is always the same. > > the MASKED part in my CEL-files looks for "all 1000_at oligos masked" > like this: > > [MASKS] > NumberCells=16 > CellHeader=X Y > 399 560 > 544 186 > 530 506 > 617 350 > 459 490 > 408 546 > 484 312 > 548 334 > 578 370 > 498 466 > 503 442 > 482 440 > 397 546 > 352 466 > 253 496 > 228 632 > > has anyone countered the sample problem? > since it seems to be same with outliers: > how do bioconductor users handle OUTLIERS and MASKED oligos? > > or am I completely wrong with what I intend to do? > > gunter > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu>