[BioC] how do people handling outliers and masked oligos?

weiss weiss at cs.uni-duesseldorf.de
Wed Oct 29 16:22:44 MET 2003


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",
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.

MASKED part in my CEL-files look like
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:

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?


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