[BioC] error in DESeq : analysis without replicates

[Wolfgang Huber]

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