[BioC] DEXSeq- ExonCountSet

[James W. MacDonald]

Hi Anitha,

The best thing to do in instances like this is to look at the help 
page. As an example, for ?read.HTSeqCounts I get:

Arguments
countfiles A string vector containing the output files with the paths 
from dexseq_count.py.

Which might be worded a bit better, but it seems clear to me that the 
expectation is that the argument is a string that tells the function 
where the output files are (and presumably these files will then be 
read into R).

Best,

Jim

On Thursday, April 10, 2014 2:01:20 PM, Anitha Sundararajan 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.
>>>
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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