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


-- 
---------------------------------------------------------------------------------------------
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@fm.ul.pt ; andreiaamaral@fc.ul.pt

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