[BioC] DEXSeq- ExonCountSet

[Anitha Sundararajan]

Thanks Jim!

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, 
"Arabidopsis_thaliana.modified.flattened.gff")

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.

Anitha

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).
>
> 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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>