[BioC] DEXSeq- ExonCountSet
James W. MacDonald
jmacdon at uw.edu
Thu Apr 10 19:23:52 CEST 2014
You haven't loaded the DEXSeq package yet (note that it isn't listed in
your sessionInfo() output).
On 4/10/2014 1:14 PM, Anitha Sundararajan wrote:
> I am a new user to DEXSeq and I was wondering if I could get some help
> resolving an error message I repeatedly get.
> I have my sample table and it looks like:
> > sampleTable
> countFile condition
> meiocyte1 Col-meiocyte-1.counts meiocytes
> meiocyte2 Col-meiocyte-2.counts meiocytes
> seedling1 Col-seedling-1.counts seedlings
> seedling2 Col-seedling-2.counts seedlings
> anther1 Col-anther-1.counts anthers
> anther2 Col-anther-2.counts anthers
> I am trying to create the ExonCountSet and I am constantly getting
> this error:
> > ecs <- read.HTSeqCounts (sampleTable$countfile, sampleTable,
> Error: could not find function "read.HTSeqCounts"
> I even tried newExonCountSet (read that in a blog) and that didn't
> work either!
> My session Info is as given:
> > sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-unknown-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=en_US.UTF-8 LC_NAME=C
>  LC_ADDRESS=C LC_TELEPHONE=C
>  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
>  parallel stats graphics grDevices utils datasets methods
>  base
> other attached packages:
>  Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0
> loaded via a namespace (and not attached):
>  hwriter_1.3 stringr_0.6.2 tools_3.0.2
> Can you please give me any insight on what might be wrong.
> Thanks so much for your help in advance
> Anitha Sundararajan.
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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