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

[Ariel Grostern]

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]]
>>
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