[BioC] siggenes: sam2html + affymetrix zebrafish

[Sam Hunter]

Thanks for the suggestion, disabling refseq seems to fix the error:

sam2html(sam.out.rma, delta.rma, "sam_out_rma.html",
cdfname="zebrafish", refseq=F)


Sam

On Wed, Jun 10, 2009 at 1:12 AM, Holger Schwender<holger.schw at gmx.de> wrote:
> Hi Sam,
>
> no, I actually have no idea. It seems that one of public repositories (entrez, ug, or one of the others) does not exist anymore. But there wasn't -- as far as I know -- a repository called GB before. So maybe some changes were made to the package annotate which is used in sam2html to get the links.
>
> I haven't installed R 2.9.0 yet, as I am currently very, very busy. So it will take some time to check where the error is. What you could do is to set all the arguments for repositories in sam2html to FALSE, and see if this works (it should). Afterwards, you might only set the repositories to TRUE which you would like to have (maybe one at a time).
>
> Another ides might be that you post this question at the BioC mailing list, as there are some guys who are more familiar with the repositories than I am.
>
> Best,
> Holger
>
> -------- Original-Nachricht --------
>> Datum: Tue, 9 Jun 2009 14:34:03 -0700
>> Von: Sam Hunter <biosam at gmail.com>
>> An: Holger Schwender <holger.schw at gmx.de>, bioconductor at stat.math.ethz.ch
>> Betreff: siggenes: sam2html + affymetrix zebrafish
>
>> Hi, I recently updated to R2.9 and after reinstalling Bioconductor
>> packages have run into the following error with annotations and the
>> sam2html function in siggenes:
>>
>> "Error in FUN(X[[1L]], ...) : unknown repository 'GB' "
>>
>> After running the following code:
>>
>> > library(siggenes)
>>
>> > sam.out.rma = sam(abatch.rma, cl=c(0,0,0,1,1,1), n.delta=20)
>>
>> > library(zebrafish.db)
>> > sam2html(sam.out.rma, delta.rma, "sam_out_rma.html",
>> +   cdfname="zebrafish")
>> Error in FUN(X[[1L]], ...) : unknown repository 'GB'
>>
>>
>>
>> This code worked in previous versions and as far as I can tell from
>> the documentation, I'm not doing anything wrong.  Any ideas?
>>
>> thanks,
>>
>> Sam
>>
>>
>> > sessionInfo()
>> R version 2.9.0 (2009-04-17)
>> x86_64-pc-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] splines   stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>>  [1] zebrafishcdf_2.4.0  annotate_1.22.0     zebrafish.db_2.2.11
>>  [4] RSQLite_0.7-1       DBI_0.2-4           AnnotationDbi_1.6.0
>>  [7] limma_2.18.1        affy_1.22.0         siggenes_1.18.0
>> [10] multtest_2.0.0      Biobase_2.4.1
>>
>> loaded via a namespace (and not attached):
>> [1] affyio_1.12.0        MASS_7.2-47          preprocessCore_1.6.0
>> [4] survival_2.35-4      tools_2.9.0          xtable_1.5-5
>
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