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Old 08-05-2014, 10:51 AM   #8
essepf
Junior Member
 
Location: Switzerland

Join Date: Aug 2014
Posts: 5
Default DESeq2 --- htseq-count

Hi Michael

Thank you for your suggestion......

Quote:
Originally Posted by Michael Love View Post
hi essepf,

Did you check the length of the count files, as Devon recommended above?

Yes...all files have 38932....

What does sampleCondition look like?

> sampleCondition
[1] pr pr pr wt wt wt
Levels: pr wt


What's your sessionInfo()

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] C

attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] BiocInstaller_1.14.2 gplots_2.14.1 ggplot2_1.0.0 DESeq_1.16.0 lattice_0.20-29 locfit_1.5-9.1 Biobase_2.24.0
[8] DESeq2_1.4.5 RcppArmadillo_0.4.320.0 Rcpp_0.11.2 GenomicRanges_1.16.4 GenomeInfoDb_1.0.2 IRanges_1.22.10 BiocGenerics_0.10.0

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.26.0 DBI_0.2-7 KernSmooth_2.23-12 MASS_7.3-33 RColorBrewer_1.0-5 RSQLite_0.11.4 XML_3.98-1.1 XVector_0.4.0
[9] annotate_1.42.1 bitops_1.0-6 caTools_1.17 colorspace_1.2-4 digest_0.6.4 gdata_2.13.3 genefilter_1.46.1 geneplotter_1.42.0
[17] grid_3.1.0 gtable_0.1.2 gtools_3.4.1 munsell_0.4.2 plyr_1.8.1 proto_0.3-10 reshape2_1.4 scales_0.2.4
[25] splines_3.1.0 stats4_3.1.0 stringr_0.6.2 survival_2.37-7 tools_3.1.0 xtable_1.7-3

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