[BioC] DEXSeq- ExonCountSet

Nicolas Delhomme nicolas.delhomme at umu.se
Thu Apr 10 20:26:39 CEST 2014


Hej Anitha!

That error means that either 1) you have a typo in your filename or 2) the file is not in your current working directory. Use getwd() to lookup your current directory and dir() to list its content.

Cheers,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Street Lab
Department of Plant Physiology
Umeå Plant Science Center

Tel: +46 90 786 7989
Email: nicolas.delhomme at umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
---------------------------------------------------------------

On 10 Apr 2014, at 15:01, Anitha Sundararajan <asundara at ncgr.org> wrote:

> 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.
>>> 
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: 
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> 
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor



More information about the Bioconductor mailing list