[BioC] gcrma error? - linked to makeProbePackage ?

Benoit Ballester benoit at ebi.ac.uk
Fri Jul 6 12:05:14 CEST 2007


James W. MacDonald wrote:
> Hi Ben,
> 
> Benoit Ballester wrote:
>> Hi,
>>
>> I am trying to use gcrma for the mouse GNF/Novartis data.
>> This dataset use a custom affy chip gnGNF1Musa. I got the CDF file and 
>> probe file from GEO.
>>
>>
>>  > library("gngnf1musacdf")
>>  > library("gngnf1musaprobe")
>>  > eset.gcrma<-gcrma(Data)
>> Adjusting for optical effect.......[more dots].....Done.
>> Computing affinitiesError: length(prlen) == 1 is not TRUE
> 
> This indicates that you have probes of more than one length (e.g., they 
> are not all 25-mers). This might have to do with what you note below, 
> that there is an extra column in your probe_tab file. However, there is 
> error checking in makeProbePackage that is supposed to catch these sorts 
> of things, so I am wondering how you were ever able to make the package 
> in the first place.
> 
> What do you get from
> 
> head(as.data.frame(gngnf1musaprobe))
> 
> Does the probe sequence column actually contain probe sequences? If not, 
> you will need to remove the extra column from your probe_tab file and 
> re-run makeProbePackage.

Hi,

This is what I have done - I have *removed* the extra column to have a 
tab file which looks like that :

AFFX-BioB-5_at 429 502 123 TCGTCAGGTGCAGGTCAGCACGTTG Antisense
AFFX-BioB-5_at 430 502 132 GCAGGTCAGCACGTTGCTGTCGATT Antisense
AFFX-BioB-5_at 431 502 138 CAGCACGTTGCTGTCGATTAAGACC Antisense
AFFX-BioB-5_at 432 502 147 GCTGTCGATTAAGACCGGAGCTTGT Antisense
AFFX-BioB-5_at 433 502 165 AGCTTGTCCGGAAGATTGCAAATAC Antisense
AFFX-BioB-5_at 434 502 177 AGATTGCAAATACTGCCCGCAAACG Antisense
AFFX-BioB-5_at 435 502 183 CAAATACTGCCCGCAAACGTCGCGC Antisense
AFFX-BioB-5_at 436 502 246 TGAACAGGTGCTGGAGTCGGCGCGC Antisense

exactly like in the HG-U95Av2_probe_tab file that is in 
matrchprobes/extdata/



I rerun the makeProbePackage again
 >  library(matchprobes)
 >  filename<-system.file("extdata","gnGNF1Musa.probe.6tab")
 >
 >  me<-"Benoit Ballester<benoit at ebi.ac.uk>"
 >  species<-"Mus_musculus"
 >
 >  makeProbePackage("gnGNF1Musa", datafile = filename, maintainer = me, 
species = species, version = "0.0.1",force = TRUE)
Importing the data.
Creating package in ./gngnf1musaprobe
Existing ./gngnf1musaprobe was removed.
Writing the data.
Checking the package.
Building the package.
[1] "gngnf1musaprobe"
Warning message:
file("") only supports open = "w+" and open = "w+b": using the former



Then I reinstall gngnf1musaprobe:

benoit at xxxx > R CMD INSTALL gngnf1musaprobe
* Installing *source* package 'gngnf1musaprobe' ...
** R
** data
** help
  >>> Building/Updating help pages for package 'gngnf1musaprobe'
      Formats: text html latex example
   gngnf1musaprobe                   text    html    latex   example
** building package indices ...
* DONE (gngnf1musaprobe)



If I look at :

 > library(gngnf1musaprobe)
 > head(as.data.frame(gngnf1musaprobe))
[1] sequence                     x
[3] y                            Probe.Set.Name
[5] Probe.Interrogation.Position Target.Strandedness
<0 rows> (or 0-length row.names)

 > gngnf1musaprobe
Object of class probetable data.frame with 0 rows and 6 columns
 > gngnf1musaprobe[1,1]
[1] NA


So I still get nothing.
Am I doing something silly when I create gngnf1musaprobe or there 
something wrong in the code ?


I have tried with the HG-U95Av2_probe_tab file from matchprobes/extdata, 
and recreated the probe env

 >  library(matchprobes)
 >  filename<-system.file("extdata"," HG-U95Av2_probe_tab")
 >
 >  me<-"Benoit Ballester<benoit at ebi.ac.uk>"
 >  species<-"Homo_sapiens"
 >  makeProbePackage("HG-U95Av2", datafile = filename, maintainer = me, 
species = species, version = "0.0.1",force = TRUE)
Importing the data.
Creating package in ./hgu95av2probe
Writing the data.
Checking the package.
Building the package.
[1] "hgu95av2probe"
Warning message:
file("") only supports open = "w+" and open = "w+b": using the former


then :
  R CMD INSTALL hgu95av2probe

back in R
 > library(hgu95av2probe)
 > hgu95av2probe
Object of class probetable data.frame with 0 rows and 6 columns.
 > hgu95av2probe[1,1]
[1] NA


Wtill nothing with the examples. Looks like my file is not the problem, 
and the problem is somewhere else.
Any ideas ?


Cheers,

Ben

-- 
Benoit Ballester, PhD



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