Hi all, I'm trying to run the Kooperberg correction on filtered data from genepix files. I've read my genepix data into and RGList (cleverly named RG) via a wt.fun function that filters out certain control spots that I don't want thrown into the analysis. In other words, I did: RG <- read.maimages(targets$FileName, source="genepix", wt.fun=filters) I now want to take this filtered data set and run kooperberg on it. The problem I'm having is that Kooperberg apparently requires a character vector containing genepix filenames as its initial argument but what I have is an RGList, not a character vector. In other words, I would like to do something like the following: > kooperberg(RG, fg="mean", bg="median", a=TRUE, layout=RGlayout) but RG is not an acceptable "names" argument. Obviously, I can't used the targets$FileName vector I used to initially read in the RGList because this is unfiltered data, and I can't use wt.fun within kooperberg. Any ideas on how to pass filtered data on to kooperberg? Thanks Matt scholz at ag.arizona.edu --------------------------------------------- College of Agriculture and Life Sciences Web Mail. http://ag.arizona.edu

Thanks for your reply, Mick. Unfortunately, I've actually tried this before: Rgmodel <- kooperberg(RG, fg="mean", bg="median", a=TRUE,layout=RGlayout) and the problem is that I get the following error message: "Error in matrix(0, ngenes, nslides) : cannot allocate vector of length 2105745408" Again, I think the problem is that kooperberg doesn't accept an RG list as a proper name argument. It would be nice if it did because there'd be no need to transfer the weights (as they are already part of RG). Matt > Hi Matt > > Hmmmm, something like this *should* work: > > # read in the data normally just to get the weights > RG <- read.maimages(targets$FileName, source="genepix", wt.fun=filters) > > # read in the data using read.series and EXACTLT THE SAME DATA FILES as > above > # ... > Rgmodel <- kooperberg(RG, fg="mean", bg="median", a=TRUE, > layout=RGlayout) > > # transfer the weights from RG to Rgmodel > Rgmodel$weights <- RG$weights > > > I think.... > > Mick > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > scholz at Ag.arizona.edu > Sent: 12 September 2005 10:59 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] another kooperberg question > > Hi all, > > I'm trying to run the Kooperberg correction on filtered data from > genepix files. > I've read my genepix data into and RGList (cleverly named RG) via a > wt.fun function that filters out certain control spots that I don't want > thrown into the analysis. In other words, I did: > > RG <- read.maimages(targets$FileName, source="genepix", wt.fun=filters) > > I now want to take this filtered data set and run kooperberg on it. The > problem I'm having is that Kooperberg apparently requires a character > vector containing genepix filenames as its initial argument but what I > have is an RGList, not a character vector. In other words, I would like > to do something like the following: > > > kooperberg(RG, fg="mean", bg="median", a=TRUE, layout=RGlayout) > > but RG is not an acceptable "names" argument. Obviously, I can't used > the targets$FileName vector I used to initially read in the RGList > because this is unfiltered data, and I can't use wt.fun within > kooperberg. Any ideas on how to pass filtered data on to kooperberg? > > Thanks > > Matt > scholz at ag.arizona.edu > > > --------------------------------------------- > College of Agriculture and Life Sciences Web Mail. > http://ag.arizona.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > --------------------------------------------- College of Agriculture and Life Sciences Web Mail. http://ag.arizona.edu

Hi Matt Hmmmm, something like this *should* work: # read in the data normally just to get the weights RG <- read.maimages(targets$FileName, source="genepix", wt.fun=filters) # read in the data using read.series and EXACTLT THE SAME DATA FILES as above # ... Rgmodel <- kooperberg(RG, fg="mean", bg="median", a=TRUE, layout=RGlayout) # transfer the weights from RG to Rgmodel Rgmodel$weights <- RG$weights I think.... Mick -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of scholz at Ag.arizona.edu Sent: 12 September 2005 10:59 To: bioconductor at stat.math.ethz.ch Subject: [BioC] another kooperberg question Hi all, I'm trying to run the Kooperberg correction on filtered data from genepix files. I've read my genepix data into and RGList (cleverly named RG) via a wt.fun function that filters out certain control spots that I don't want thrown into the analysis. In other words, I did: RG <- read.maimages(targets$FileName, source="genepix", wt.fun=filters) I now want to take this filtered data set and run kooperberg on it. The problem I'm having is that Kooperberg apparently requires a character vector containing genepix filenames as its initial argument but what I have is an RGList, not a character vector. In other words, I would like to do something like the following: > kooperberg(RG, fg="mean", bg="median", a=TRUE, layout=RGlayout) but RG is not an acceptable "names" argument. Obviously, I can't used the targets$FileName vector I used to initially read in the RGList because this is unfiltered data, and I can't use wt.fun within kooperberg. Any ideas on how to pass filtered data on to kooperberg? Thanks Matt scholz at ag.arizona.edu --------------------------------------------- College of Agriculture and Life Sciences Web Mail. http://ag.arizona.edu _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

Hi Matt Read in the data normally using: RG <- read.maimages(etc etc) Then read in the data *again*, using the commands I sent you a while ago ie: read.series(etc) RGmodel <- kooperberg(etc) IE do NOT pass RG to the kooperberg function. The weights from RG should transfer easily across to RGmodel. Mick -----Original Message----- From: scholz at Ag.arizona.edu [mailto:scholz at Ag.arizona.edu] Sent: Wed 14/09/2005 11:13 AM To: michael watson (IAH-C); scholz at Ag.arizona.edu; bioconductor at stat.math.ethz.ch Cc: Subject: RE: [BioC] another kooperberg question Thanks for your reply, Mick. Unfortunately, I've actually tried this before: Rgmodel <- kooperberg(RG, fg="mean", bg="median", a=TRUE,layout=RGlayout) and the problem is that I get the following error message: "Error in matrix(0, ngenes, nslides) : cannot allocate vector of length 2105745408" Again, I think the problem is that kooperberg doesn't accept an RG list as a proper name argument. It would be nice if it did because there'd be no need to transfer the weights (as they are already part of RG). Matt > Hi Matt > > Hmmmm, something like this *should* work: > > # read in the data normally just to get the weights > RG <- read.maimages(targets$FileName, source="genepix", wt.fun=filters) > > # read in the data using read.series and EXACTLT THE SAME DATA FILES as > above > # ... > Rgmodel <- kooperberg(RG, fg="mean", bg="median", a=TRUE, > layout=RGlayout) > > # transfer the weights from RG to Rgmodel > Rgmodel$weights <- RG$weights > > > I think.... > > Mick > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > scholz at Ag.arizona.edu > Sent: 12 September 2005 10:59 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] another kooperberg question > > Hi all, > > I'm trying to run the Kooperberg correction on filtered data from > genepix files. > I've read my genepix data into and RGList (cleverly named RG) via a > wt.fun function that filters out certain control spots that I don't want > thrown into the analysis. In other words, I did: > > RG <- read.maimages(targets$FileName, source="genepix", wt.fun=filters) > > I now want to take this filtered data set and run kooperberg on it. The > problem I'm having is that Kooperberg apparently requires a character > vector containing genepix filenames as its initial argument but what I > have is an RGList, not a character vector. In other words, I would like > to do something like the following: > > > kooperberg(RG, fg="mean", bg="median", a=TRUE, layout=RGlayout) > > but RG is not an acceptable "names" argument. Obviously, I can't used > the targets$FileName vector I used to initially read in the RGList > because this is unfiltered data, and I can't use wt.fun within > kooperberg. Any ideas on how to pass filtered data on to kooperberg? > > Thanks > > Matt > scholz at ag.arizona.edu > > > --------------------------------------------- > College of Agriculture and Life Sciences Web Mail. > http://ag.arizona.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > --------------------------------------------- College of Agriculture and Life Sciences Web Mail. http://ag.arizona.edu