error in nbinomTest from package DESeq
1
0
Entering edit mode
@andreia-fonseca-3796
Last seen 7.1 years ago
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 [[alternative HTML version deleted]]
DESeq DESeq • 966 views
ADD COMMENT
0
Entering edit mode
@andreia-fonseca-3796
Last seen 7.1 years ago
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 [[alternative HTML version deleted]]
ADD COMMENT
0
Entering edit mode
Dear Wolfgang, just to say no error with last version of the package. kind regards, Andreia On Thu, Jul 8, 2010 at 11:15 PM, Andreia Fonseca <andreia.fonseca@gmail.com>wrote: > 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 > -- -------------------------------------------- Andreia J. Amaral Unidade de Imunologia Clínica Instituto de Medicina Molecular Universidade de Lisboa email: andreiaamaral@fm.ul.pt andreia.fonseca@gmail.com [[alternative HTML version deleted]]
ADD REPLY

Login before adding your answer.

Traffic: 960 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6