On Wed, Jun 16, 2004 at 05:08:51PM +0200, Michael Seewald wrote: > > Dear Wolfgang, dear Robert, > > It seems that the vignette of matchprobes is broken. I am using 1.9.1 alpha > (2004-05-25) and matchprobes 1.0.8. This is what I get: > > > library(affy) > > library(matchprobes) > > openVignette() > Please select (by number) a vignette > 1: Handling probe sequence information > 2: Biobase Primer > 3: Howto Bioconductor > 4: HowTo HowTo > 5: esApply Introduction > Selection: 1 > Error in switch(ext[length(ext)], pdf = openPDF(vigFiles[index]), html = > browseURL(paste("file://", : > Don't know how to handle this vignette > > Are you able to open any of the vignettes? And, do you in fact have a pdf for this vignette? You can tell by looking in the directory that the R library is installed in .libPaths() will tell you the root, then from there look in matchprobes/doc and you should see matchprobes.pdf you may not have your pdf viewer properly set, options("pdfviewer") should be checked > > Any help is appreciated! > > Thanks a lot & best wishes, > Michael -- +--------------------------------------------------------------------- ------+ | 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.harvard.edu | +--------------------------------------------------------------------- ------+

Dear Robert, On Wed, 16 Jun 2004, Robert Gentleman wrote: > Are you able to open any of the vignettes? Yes, all of them work (under Windows or Linux) usually. > And, do you in fact have a pdf > for this vignette? That seems to be it. Neither matchprobes.tar.gz nor matchprobes.zip that are linked under http://www.bioconductor.org/repository/release1.4/package/html/matchpr obes.html contain a pdf document. Thanks & best wishes, Michael

Dear Robert, dear Bioconductor people, I would like to use combineAffyBatch to merge a dataset of Affymetrix HG-U133Plus2 and HG-U133A arrays. The main point here is the comparison of the two arrays - and possibly generation of a unified dataset that is valid for further analysis. (Disposing half of the Plus2 information is not of concern for now..) So far I used the following to combine and normalize with RMA (works great!): # DATA.133A, DATA.133Plus are generated by ReadAffy() > DATA.combine <- combineAffyBatch( list(DATA.133A,DATA.133Plus), + c("hgu133aprobe","hgu133plus2probe"), + newcdf="newcdfenv", verbose=T + ) > newcdfenv <- DATA.combine$cdf > DATA.A.RMA <- rma(DATA.combine$dat) Then I run into trouble because (I believe) I have to work with the cdf environment: > DATA.A.GCRMA <- gcrma(DATA.A) Computing affinitiesError in library(cdfpackagename, character.only = TRUE) : There is no package called 'newcdfenvcdf' I tried also: > ai <- compute.affinities(cdfname="newcdfenv",verbose=T) Error in library(cdfpackagename, character.only = TRUE) : There is no package called 'newcdfenvcdf' How can I create the correct "newcdfenvcdf"? And why doesn't specifying "newcdfenv" not help? Best wishes, Michael