[BioC] AnnotationDbi:makeProbePackage for PM-only chips....getting closer.....now error in installation of probe package

[James W. MacDonald]

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]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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