[BioC] DEXSeq- ExonCountSet
Anitha Sundararajan
asundara at ncgr.org
Thu Apr 10 22:00:03 CEST 2014
Thanks so much for your response(s)
I went back a did a couple of things and looks like I now have the exon
count set.
So I was running R in the same directory as the file(s) location. I
still went ahead and specified the complete path for each file and I
still got the same error message.
I then took a look at the help page (?read.HTSeqCounts) per Jim's
suggestion and defined a design file additionally. That seemed to work.
Please see my commands below (just for reference)
sampleTable <- data.frame (row.names=c("meiocyte1", "meiocyte2",
"seedling1", "seedling2", "anther1", "anther2"),
countFile=c("/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col-meiocyte-1.counts",
"/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col-meiocyte-2.counts",
"/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col-seedling-1.counts",
"/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col-seedling-2.counts",
"/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col-anther-1.counts",
"/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col-anther-2.counts"),
condition= c("meiocytes", "meiocytes", "seedlings", "seedlings",
"anthers", "anthers"),stringsAsFactors=FALSE,check.names=FALSE)
> file.exists(sampleTable$countFile)
[1] TRUE TRUE TRUE TRUE TRUE TRUE
countFiles <- sampleTable$countFile
design <- sampleTable[,-1]
> ecs <- read.HTSeqCounts(countFiles, design,
"/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Arabidopsis_thaliana.modified.flattened.gff")
> ecs
ExonCountSet (storageMode: environment)
assayData: 171805 features, 6 samples
element names: counts
protocolData: none
phenoData
sampleNames:
/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col-meiocyte-1.counts
/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col-meiocyte-2.counts
...
/home/projects/opal-maize/arabidopsis_MARCH032014/DEXSeq/Col-anther-2.counts
(6 total)
varLabels: sizeFactor condition countfiles
varMetadata: labelDescription
featureData
featureNames: AT1G01010:E001 AT1G01010:E002 ... ATMG01410:E001
(171805 total)
fvarLabels: geneID exonID ... transcripts (13 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
Thanks again for all your input. Hoping to run this through completion
with few problems :)
Anitha
On 4/10/14 12:26 PM, Nicolas Delhomme wrote:
> 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.
>>>>
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