Hi James, That worked well. Thanks for your help, Ariel On Tue, 28 Jun 2011 10:05:51 -0400, "James W. MacDonald" <jmacdon at="" med.umich.edu=""> wrote: > Hi Ariel, > > Use > > makeProbePackage("cb1190a520768f", > datafile=gzfile(filename,open="r"),outdir=outdir,maintainer=me,species =species, > version="1.0",check = FALSE, comparewithcdf = FALSE, force = TRUE, build > = FALSE) > > then when it is done, open a terminal prompt and do > > /path/to/R/bin/R CMD build cb1190a520768fprobe > /path/to/R/bin/R CMD check cb1190a520768fprobe_1.0.tar.gz > /path/to/R/bin/R CMD INSTALL cb1190a520768fprobe_1.0.tar.gz > > or you could just install and forgo the checking > > /path/to/R/bin/R CMD INSTALL cb1190a520768fprobe > > Best, > > Jim > > > > On 6/27/2011 9:55 PM, Ariel Grostern wrote: >> >> >> Hello, >> >> I am using R 2.10.0. The sessionInfo data is below at the end >> of this message. I am using Ubuntu 10.04. >> >> I am trying to make a probe >> package for a PM only Affy chip. I have altered the code for >> AnnotationDbi's makeProbePackage.R to not look for MM probes (see code >> pasted below). Then I installed the AnnotationDbi package from source, >> and >> tried to prepare the package from my probe_tab file. >> >> Here is my code: >> >>> >> filename outdir me species makeProbePackage("cb1190a520768f", >> datafile=gzfile(filename,open="r"),outdir=outdir,maintainer=me,species =species,version="1.0",force=TRUE)Importing >> the data. >> Loading required package: >> affy >> ********************************************************************** ***** >> >> Found different probe set names in 'CDF package' and 'probe package' for >> >> 4800 probes. >> AFFX-BkGr-GC19_at PsedDRAFT_3064_at >> PsedDRAFT_0240_at >> PsedDRAFT_3209_at >> PsedDRAFT_3109_at AFFX-BkGr-GC12_at >> PsedDRAFT_5914_at >> PsedDRAFT_2727_at >> AFFX-BkGr-GC16_at AFFX-BkGr-GC19_at >> PsedDRAFT_1308_at >> PsedDRAFT_4982_at >> AFFX-BkGr-GC17_at AFFX-BkGr-GC19_at >> PsedDRAFT_6011_at >> AFFX-TrpnX-M_at >> PsedDRAFT_6222_at PsedDRAFT_0240_at >> AFFX-BkGr-GC16_at >> PsedDRAFT_2460_at >> If you consider this mismatch insignificant, you may >> want to rerun this >> function with 'comparewithcdf = FALSE'. Otherwise, >> you'll need to >> figure out the reason for this! >> Error in >> .lgExtraParanoia(pt, cdfname) : Stopped >> In addition: Warning messages: >> 1: >> closing unused connection 5 >> (/home/bioinformatics/R/x86_64-pc-linux-gnu- library/2.10/AnnotationDbi/extdata/CB1190a520768F_probe_tab.gz) >> >> 2: closing unused connection 4 >> (/home/bioinformatics/R/x86_64-pc-linux-gnu- library/2.10/AnnotationDbi/extdata/CB1190a520768F_probe_tab.gz) >> >> 3: closing unused connection 3 >> (/home/bioinformatics/R/x86_64-pc-linux-gnu- library/2.10/AnnotationDbi/extdata/CB1190a520768F_probe_tab.gz) >> >> >> ---->Not sure why my CDF and probe list don't match - both were obtained >> from Affymetrix.......So then I ran: >> >>> makeProbePackage("cb1190a520768f", >> datafile=gzfile(filename,open="r"),outdir=outdir,maintainer=me,species =species,version="1.0",force=TRUE, >> comparewithcdf=FALSE) >> Importing the data. >> Creating package in >> /tmp/RtmpJxjLDw/cb1190a520768fcdfprobe >> Writing the data. >> Checking the >> package. >> Error in makeProbePackage("cb1190a520768fcdf", datafile = >> gzfile(filename, : >> * checking whether package 'cb1190a520768fcdfprobe' >> can be installed ... ERROR >> >> It looks like R wants to install the package, >> but there is an unknown error. I though that maybe it was because i >> didn't >> have administrative authority to write files, so i entered R by "sudo R", >> but still the same thing. >> >> I would like to figure out what the error >> pertains to.....Does any one have any pointers? >> >> Thanks, >> >> Ariel >> >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 >> LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] >> LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] >> LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base >> packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other >> attached packages: >> [1] cb1190a520768fcdf_1.24.0 affy_1.24.2 >> AnnotationDbi_1.14.1 >> [4] Biobase_2.6.1 >> >> loaded via a namespace (and not >> attached): >> [1] affyio_1.14.0 DBI_0.2-5 preprocessCore_1.8.0 >> [4] >> RSQLite_0.9-2 tools_2.10.1 >> >> ## On most chips, PM and MM probe are next to >> each other on the chip, at same >> ## x coordinate and at adjacent y >> coordinates. Then, "sizex" is always the same, >> ## namely the size of the >> chip in x-direction. On some chips, there are few >> ## exceptions. >> ##tab = >> table(mm1-pm1) >> tab = table(pm1) >> ## WHAT TO DO FOR THE ABOVE LINE? >> sizex >> = as.numeric(names(tab))[ max(tab)==tab ] >> >> ## The probe indices according >> to pt >> pm2 = pt$y * sizex + pt$x + 1 >> ## Crossed out the mm2 function >> ## >> mm2 = (pt$y+1) * sizex + pt$x + 1 >> psnm2 = pt[["Probe.Set.Name"]] >> >> ## >> Check if the probe set names that are associated with each probe >> ## are >> the same in both CDF and pt >> ## z1 = z2 = rep(NA, max(pm1, mm1, pm2, mm2)) >> >> ## z1[pm1] = z1[mm1] = psnm1 >> ## z2[pm2] = z2[mm2] = psnm2 >> ## Remove mm1 >> and mm3 referals >> z1 = z2 = rep(NA, max(pm1, pm2)) >> z1[pm1] = psnm1 >> z2[pm2] = >> psnm2 >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor