[BioC] DEXSeq- ExonCountSet

Anitha Sundararajan asundara at ncgr.org
Thu Apr 10 19:14:45 CEST 2014


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 

 > 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 

My session Info is as given:

 > sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=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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