Dear Wolfgang,

please disregard my last email, it was missing package xtable, DESeq is
loaded now.
with kind regards
Andreia

On Thu, Jul 8, 2010 at 10:44 PM, Andreia Fonseca
<andreia.fonseca@gmail.com>wrote:

> Dear Wolfgang,
>
> I am using a windows machine and I just have installed R 2.11.1 and I am
> trying to install the last version of DESeq. The installation seems ok but I
> am getting an error while uploading the library:
>
> library(DESeq)
> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
>   there is no package called 'xtable'
> Error: package/namespace load failed for 'DESeq'
>
> maybe there is a bug?
>
> thanks for the help
> kind regards,
> Andreia
>
>
> On Tue, Jun 29, 2010 at 4:57 PM, Wolfgang Huber <whuber@embl.de> wrote:
>
>> Dear Andreia
>>
>> Thank you for the feedback!
>>
>> The first thing to do here is to use a more recent version of DESeq (last
>> release was 1.0.4, the current devel is 1.1.5).
>>
>> If that fails, the second is to make available (e.g. by using the "dump"
>> function in R or by posting the saved "countsTable_pi" object on a
>> http-server) the offending data so that we can reproduce your problem.
>>
>>        Best wishes
>>        Wolfgang
>>
>>
>> On Jun/21/10 6:48 PM, Andreia Fonseca wrote:
>>
>>> Dear all,
>>>
>>> I am using DESeq package to analyze differences of expression of miRNA
>>> from
>>> short sequence data.
>>> I have a subset of sequences for which I am analyzing differences between
>>> treatment NS vs treatment S
>>> the code I am using is
>>> conds_celltype<-c("NS","NS","NS","S","S","S","S","S","S")
>>> cds_pi_ct<-newCountDataSet(countsTable_pi,conds_celltype)
>>> cds_pi_ct<-estimateSizeFactors(cds_pi_ct)
>>> sizeFactors(cds_pi_ct)
>>> cds_pi_ct<-estimateVarianceFunctions(cds_pi_ct)
>>> res_pi_ct<-nbinomTest(cds_pi_ct,"NS","S")
>>> resSig_pi_ct<-res_pi_ct[res_pi_ct$padj<.1,]
>>> resSig_pi_ct
>>>
>>> but I am getting an error message when I am making the test,
>>>
>>> res_pi_ct<-nbinomTest(cds_pi_ct,"NS","S")
>>> Error: is.finite(pobs) is not TRUE
>>> In addition: Warning message:
>>> In dnbinom(x, size, prob, log) : NaNs produced
>>>
>>>
>>> I don't understand this, I have used this code for another subset of
>>> sequences and it worked just fine. Can someone tell me what I am doing
>>> wrong?
>>> Thanks
>>> Andreia
>>>
>>> Session Info:
>>>
>>>  sessionInfo()
>>> R version 2.10.1 (2009-12-14)
>>> i386-pc-mingw32
>>>
>>> locale:
>>> [1] LC_COLLATE=Portuguese_Portugal.1252
>>> LC_CTYPE=Portuguese_Portugal.1252    LC_MONETARY=Portuguese_Portugal.1252
>>> [4] LC_NUMERIC=C                         LC_TIME=Portuguese_Portugal.1252
>>>
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices datasets  utils     methods   base
>>>
>>> other attached packages:
>>> [1] DESeq_0.7.12    locfit_1.5-6    lattice_0.17-26 akima_0.5-4
>>> Biobase_2.6.1
>>>
>>> loaded via a namespace (and not attached):
>>>  [1] annotate_1.24.1     AnnotationDbi_1.8.2 DBI_0.2-5
>>> genefilter_1.28.2   geneplotter_1.24.0  grid_2.10.1
>>>  [7] RColorBrewer_1.0-2  RSQLite_0.8-4       splines_2.10.1
>>> survival_2.35-7     xtable_1.5-6
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor@stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>> --
>>
>>
>> Wolfgang Huber
>> EMBL
>> http://www.embl.de/research/units/genome_biology/huber
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>
>
> --
> --------------------------------------------
> Andreia J. Amaral
> Unidade de Imunologia Clínica
> Instituto de Medicina Molecular
> Universidade de Lisboa
> email: andreiaamaral@fm.ul.pt
>          andreia.fonseca@gmail.com
>



-- 
--------------------------------------------
Andreia J. Amaral
Unidade de Imunologia Clínica
Instituto de Medicina Molecular
Universidade de Lisboa
email: andreiaamaral@fm.ul.pt
         andreia.fonseca@gmail.com

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