[BioC] DEXSeq- ExonCountSet
asundara at ncgr.org
Thu Apr 10 20:01:20 CEST 2014
I should have noticed that. I had to import paths for R, gcc and other
libs and re-load the package. That solved it.
But I am running into another problem at the same step.
When I run
ecs <- read.HTSeqCounts(sampleTable$countFile, sampleTable,
I now get,
Error in read.table(x, header = FALSE, stringsAsFactors = FALSE) :
'file' must be a character string or connection
Can you please help me out with this error.
Thanks again for your prompt response.
On 4/10/14 11:23 AM, James W. MacDonald wrote:
> Hi Anitha,
> You haven't loaded the DEXSeq package yet (note that it isn't listed
> in your sessionInfo() output).
> On 4/10/2014 1:14 PM, Anitha Sundararajan wrote:
>> I am a new user to DEXSeq and I was wondering if I could get some
>> help resolving an error message I repeatedly get.
>> I have my sample table and it looks like:
>> > sampleTable
>> countFile condition
>> meiocyte1 Col-meiocyte-1.counts meiocytes
>> meiocyte2 Col-meiocyte-2.counts meiocytes
>> seedling1 Col-seedling-1.counts seedlings
>> seedling2 Col-seedling-2.counts seedlings
>> anther1 Col-anther-1.counts anthers
>> anther2 Col-anther-2.counts anthers
>> I am trying to create the ExonCountSet and I am constantly getting
>> this error:
>> > ecs <- read.HTSeqCounts (sampleTable$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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