[BioC] error in DESeq : analysis without replicates

[Wolfgang Huber]

Dear Andreia

I am glad to hear it worked out.

What I meant to say, please do not take the p-values serious that you 
get from this analysis. For ranking, it may be useful. (Although one 
would not really need DESeq for that.)

Good luck with the follow-up analysis -

	Wolfgang






Sep/3/12 11:54 PM, Andreia Fonseca scripsit:
> Dear Wolfgang,
>
> thanks for the reply. In the meanwhile I solved the problem by
> eliminating the transcripts that had <2000 reads in one of the
> conditions. Then it worked without any problems.
>
> Kind regards,
>
> Andreia
>
> PS: why would I blame the package? I must say that we have been having
> many reproducible results from analysis without replicates. And I am
> satisfied with it.
> Of course there can be a lot of false positives in transcripts with low
> read counts and small fold changes....and I am aware of that....
>
> On Mon, Sep 3, 2012 at 9:46 PM, Wolfgang Huber <whuber at embl.de
> <mailto:whuber at embl.de>> wrote:
>
>     Dear Andreia,
>
>     have a look at the error message that was produced, it might point
>     you to the fact that the argument 'condB' that you provided to
>     'binomTest' does not match the condition names that you used for the
>     cds_T1_2 object.
>
>     It would be unusual if the results of such an analysis of these data
>     were to make a lot of sense; if they do not, please do not blame the
>     tool (DESeq) for it.
>
>     Btw, please in the future provide a reproducible example (in below
>     post, you did not tell us how you called the function 'nbinomTest',
>     and the object 'first' was undefined).
>
>              Best wishes
>              Wolfgang
>
>
>
>
>     Sep/3/12 5:22 PM, Andreia Fonseca scripsit:
>
>         Dear list,
>
>         I am trying analysis without replicates for a large data set of
>         small
>         transcripts and I am getting the following error
>
>         Error: condB %in% levels(conditions(cds)) is not TRUE
>
>         the code that I have used is
>
>         myvars_2<-c("transcript","T1",__"T2")
>         first_T1_2<-first[myvars_2]
>         countsTable_T1_2<-first_T1_2
>         countsTable_T1_2<-countsTable___T1_2[,-1]
>         rownames(countsTable_T1_2)<-__first_T1_2$transcript
>         #script for DEA
>         library(DESeq)
>
>         #estimate dispersions
>
>         conds <- c("NS","NS_HIV1")
>
>         cds_T1_2<-newCountDataSet(__countsTable_T1_2, conds)
>         cds_T1_2<-estimateSizeFactors(__cds_T1_2)
>         sizeFactors(cds_T1_2)
>
>         cds_T1_2<-estimateDispersions(__cds_T1_2,
>         method="blind",fitType="local"__,sharingMode="fit-only")
>
>         the dataset has 3965346 transcripts.
>
>         can someone help?
>
>         thanks
>
>
>         R version 2.15.0 (2012-03-30)
>         Platform: x86_64-redhat-linux-gnu (64-bit)
>
>         locale:
>            [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>            [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>            [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>            [7] LC_PAPER=C                 LC_NAME=C
>            [9] LC_ADDRESS=C               LC_TELEPHONE=C
>         [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>         attached base packages:
>         [1] stats     graphics  grDevices utils     datasets  methods   base
>
>         other attached packages:
>         [1] DESeq_1.8.3        locfit_1.5-8       Biobase_2.16.0
>         BiocGenerics_0.2.0
>         [5] reshape_0.8.4      plyr_1.7.1
>
>         loaded via a namespace (and not attached):
>            [1] annotate_1.34.1      AnnotationDbi_1.18.1 DBI_0.2-5
>            [4] genefilter_1.38.0    geneplotter_1.34.0   grid_2.15.0
>            [7] IRanges_1.14.4       lattice_0.20-10      RColorBrewer_1.0-5
>         [10] RSQLite_0.11.1       splines_2.15.0       stats4_2.15.0
>         [13] survival_2.36-14     tools_2.15.0         XML_3.9-4
>         [16] xtable_1.7-0
>
>
>
>
>     --
>     Best wishes
>              Wolfgang
>
>     Wolfgang Huber
>     EMBL
>     http://www.embl.de/research/__units/genome_biology/huber
>     <http://www.embl.de/research/units/genome_biology/huber>
>
>     _________________________________________________
>     Bioconductor mailing list
>     Bioconductor at r-project.org <mailto:Bioconductor at r-project.org>
>     https://stat.ethz.ch/mailman/__listinfo/bioconductor
>     <https://stat.ethz.ch/mailman/listinfo/bioconductor>
>     Search the archives:
>     http://news.gmane.org/gmane.__science.biology.informatics.__conductor <http://news.gmane.org/gmane.science.biology.informatics.conductor>
>
>
>
>
> --
> ---------------------------------------------------------------------------------------------
> Andreia J. Amaral, PhD
> BioFIG - Center for Biodiversity, Functional and Integrative Genomics
> Instituto de Medicina Molecular
> University of Lisbon
> Tel: +352 217500000 (ext. office: 28253)
> email:andreiaamaral at fm.ul.pt <mailto:email%3Aandreiaamaral at fm.ul.pt> ;
> andreiaamaral at fc.ul.pt <mailto:andreiaamaral at fc.ul.pt>
>


-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber