[BioC] error in DESeq : analysis without replicates
whuber at embl.de
Mon Sep 3 22:46:56 CEST 2012
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).
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
> #script for DEA
> #estimate dispersions
> conds <- c("NS","NS_HIV1")
> cds_T1_2<-newCountDataSet(countsTable_T1_2, conds)
> the dataset has 3965346 transcripts.
> can someone help?
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>  LC_PAPER=C LC_NAME=C
>  LC_ADDRESS=C LC_TELEPHONE=C
>  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  DESeq_1.8.3 locfit_1.5-8 Biobase_2.16.0
>  reshape_0.8.4 plyr_1.7.1
> loaded via a namespace (and not attached):
>  annotate_1.34.1 AnnotationDbi_1.18.1 DBI_0.2-5
>  genefilter_1.38.0 geneplotter_1.34.0 grid_2.15.0
>  IRanges_1.14.4 lattice_0.20-10 RColorBrewer_1.0-5
>  RSQLite_0.11.1 splines_2.15.0 stats4_2.15.0
>  survival_2.36-14 tools_2.15.0 XML_3.9-4
>  xtable_1.7-0
More information about the Bioconductor