Hi: With ReadAffy, Affy can mask the outliers as NA with option: rm.outlier=TRUE. But I could not do RMA or MAS 5 estimation with AffyBatch obtained in this way. either using rma or using expresso, as I always got the error message about NA/NaN: >background correction: mas >PM/MM correction : mas >expression values: mas >background correcting...Error in as.vector(data) : NA/NaN/Inf in foreign function call (arg 1) Has anyone used outlier information during the expression estimation? I searched all the mailing list archieve, but found no mention on if this information is use or not, or information on if outliers marked as NA allowed in estimation. Thank you for your time. Lishuang Shen BarleyBase, Iowa State University Ames, Iowa 50010 Tel: (515)-294-8479 (Office Email: lshen@iastate.edu; shen_lishuang@yahoo.com

The handling of NAs in not implemented for all the processing methods, unfortunately. We had some discussions about that around the first release, agreed that it would be cool to have it for all, but ... it never went top priority since few appear to use the feature (or may be few do so 'cause it's not working in every case). Other may correct me, I think that skipping the background correction for now should make it through (for mas, may be for rma too). If you really-really-really what it to work and come with a fix, it would be neat too... Sorry, not much more to suggest for now... Hopin' it helps, Laurent On Wed, Jul 16, 2003 at 02:35:05PM -0500, Lishuang Shen wrote: > Hi: > > With ReadAffy, Affy can mask the outliers as NA with option: rm.outlier=TRUE. > > But I could not do RMA or MAS 5 estimation with AffyBatch obtained in this way. > either using rma or using expresso, as I always got the error message about > NA/NaN: > > >background correction: mas > >PM/MM correction : mas > >expression values: mas > >background correcting...Error in as.vector(data) : NA/NaN/Inf in foreign > function call (arg 1) > > Has anyone used outlier information during the expression estimation? I > searched all the mailing list archieve, but found no mention on if this > information is use or not, or information on if outliers marked as NA allowed > in estimation. > > > Thank you for your time. > > > Lishuang Shen > > BarleyBase, > Iowa State University > Ames, Iowa 50010 > Tel: (515)-294-8479 (Office > Email: lshen@iastate.edu; shen_lishuang@yahoo.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Dear Laurent and Ben: Thank you for the quick and instructive replies. Yes, most CEL files has very little fraction of outlier cell, so it should not cause much difference. Just that I came across a data set, with >5000 cells labled as outlier (>2% of total cells). Then I thought it might make difference with outlier information for it. I will evaluate the need and decide if take outliers into consideration in analysis or to do it someway. Regards, Lishuang > The handling of NAs in not implemented for all the processing methods, > unfortunately. We had some discussions about that around the > first release, agreed that it would be cool to have it for all, > but ... it never went top priority since few appear to use the > feature (or may be few do so 'cause it's not working in every case). > Other may correct me, I think that skipping the background correction > for now should make it through (for mas, may be for rma too). > If you really-really-really what it to work and come with a fix, > it would be neat too... > > Sorry, not much more to suggest for now... > > > > Hopin' it helps, > > > > Laurent > > > > > > On Wed, Jul 16, 2003 at 02:35:05PM -0500, Lishuang Shen wrote: > > Hi: > > > > With ReadAffy, Affy can mask the outliers as NA with option: rm.outlier=TRUE. > > > > But I could not do RMA or MAS 5 estimation with AffyBatch obtained in this way. > > either using rma or using expresso, as I always got the error message about > > NA/NaN: > > > > >background correction: mas > > >PM/MM correction : mas > > >expression values: mas > > >background correcting...Error in as.vector(data) : NA/NaN/Inf in foreign > > function call (arg 1) > > > > Has anyone used outlier information during the expression estimation? I > > searched all the mailing list archieve, but found no mention on if this > > information is use or not, or information on if outliers marked as NA allowed > > in estimation. > > > > > > Thank you for your time. > > > > > > Lishuang Shen > > > > BarleyBase, > > Iowa State University > > Ames, Iowa 50010 > > Tel: (515)-294-8479 (Office > > Email: lshen@iastate.edu; shen_lishuang@yahoo.com > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > >