[BioC] DEXSeq- ExonCountSet

[James W. MacDonald]

Hi Anitha,

You haven't loaded the DEXSeq package yet (note that it isn't listed in 
your sessionInfo() output).

Best,

Jim


On 4/10/2014 1:14 PM, Anitha Sundararajan wrote:
> Hi
>
> 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, 
> "Arabidopsis_thaliana.modified.flattened.gff")
> 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)
>
> 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=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets methods
> [8] base
>
> other attached packages:
> [1] Biobase_2.22.0       BiocGenerics_0.8.0   BiocInstaller_1.12.0
>
> loaded via a namespace (and not attached):
> [1] 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.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099