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