Hi, Couple of questions regarding the bioconductor packages and the handling of missing values. 1. Is there a currently an impute function implementation( or likelihood of adding an impute function)? 2. Does the exprSet object have a restriction of having missing values in the "exprs" slot ? Thanks Shyam

On Tue, Oct 29, 2002 at 12:33:17PM -0500, Sundaram, Shyam (NIH/CIT) wrote: > Hi, > Couple of questions regarding the bioconductor packages and the handling of > missing values. > > 1. Is there a currently an impute function implementation( or likelihood of > adding an impute function)? It is unclear what such a function would do. In most cases one is going to have to use some reasonable amount of external information to perform imputations. This is possible now. > 2. Does the exprSet object have a restriction of having missing values in > the "exprs" slot ? Not intentionally (and not that I am aware of). If you have a specific example please post it. If you are simply wondering then I suggest that you actually try it and find out. There are lots of runnable examples that can easily be adjusted to produce missing values and without too much effort you can see the answer for yourself. Robert > > Thanks > Shyam > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+

In the PAML package for R of Tibshirani (Shrunken Centroid Learning) they have used K-nearest neighbour imputation. Obviously you should not use this if there are too many missing values, but then most sensible people will choose to reject an experiment if it is too corrupted prior to this. Stephen Henderson Wolfson institute for Biomedical Research UCL, Gower Street, WC1E 6BT, UK 44 (0)207 679 6827 -----Original Message----- From: Robert Gentleman To: Sundaram, Shyam (NIH/CIT) Cc: 'bioconductor@stat.math.ethz.ch' Sent: 29/10/02 20:56 Subject: Re: [BioC] Handling Missing Values On Tue, Oct 29, 2002 at 12:33:17PM -0500, Sundaram, Shyam (NIH/CIT) wrote: > Hi, > Couple of questions regarding the bioconductor packages and the handling of > missing values. > > 1. Is there a currently an impute function implementation( or likelihood of > adding an impute function)? It is unclear what such a function would do. In most cases one is going to have to use some reasonable amount of external information to perform imputations. This is possible now. > 2. Does the exprSet object have a restriction of having missing values in > the "exprs" slot ? Not intentionally (and not that I am aware of). If you have a specific example please post it. If you are simply wondering then I suggest that you actually try it and find out. There are lots of runnable examples that can easily be adjusted to produce missing values and without too much effort you can see the answer for yourself. Robert > > Thanks > Shyam > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- -- ----+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- -- ----+ _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor ********************************************************************** This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager (wibr.mail@ucl.ac.uk). All files are scanned for viruses. **********************************************************************