[BioC] DEXSeq- fitDispersionFunction error
Anitha Sundararajan
asundara at ncgr.org
Wed Jul 30 00:15:36 CEST 2014
I re-ran some steps so you can see the output-
Please see complete code below-
============================
>source("http://bioconductor.org/biocLite.R")
>biocLite("DEXSeq")
>library ("DEXSeq")
>library("parallel")
>sampleTable.conVsgigi <- data.frame (row.names=c("control1",
"control2", "control3", "Gigi1", "Gigi2", "Gigi3"),
countFile=c("/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root-1.counts",
"/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root-2.counts",
"/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root-3.counts",
"/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root_Gigi-1.counts",
"/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root_Gigi-2.counts",
"/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root_Gigi-3.counts"),
condition=c("control", "control", "control", "Gigi", "Gigi", "Gigi"),
stringsAsFactors=FALSE, check.names=FALSE)
>sampleTable.conVsgigi
countFile
control1
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root-1.counts
control2
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root-2.counts
control3
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root-3.counts
Gigi1
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root_Gigi-1.counts
Gigi2
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root_Gigi-2.counts
Gigi3
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root_Gigi-3.counts
condition
control1 control
control2 control
control3 control
Gigi1 Gigi
Gigi2 Gigi
Gigi3 Gigi
>file.exists(sampleTable.conVsgigi$countFile)
>sapply (sampleTable.conVsgigi, class)
>countFiles.conVsgigi <- sampleTable.conVsgigi$countFile
>head (countFiles.conVsgigi)
[1]
"/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root-1.counts"
[2]
"/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root-2.counts"
[3]
"/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root-3.counts"
[4]
"/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root_Gigi-1.counts"
[5]
"/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root_Gigi-2.counts"
[6]
"/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root_Gigi-3.counts"
>design.conVsgigi <- sampleTable.conVsgigi[,-1]
>ecs.ConVsgigi <- read.HTSeqCounts (countFiles.conVsgigi,
design.conVsgigi,
"/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/Mt4.0v1_genes_20130731_1800.Flattened.gff")
>ecs.ConVsgigi
ExonCountSet (storageMode: environment)
assayData: 228882 features, 6 samples
element names: counts
protocolData: none
phenoData
sampleNames:
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root-1.counts
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root-2.counts
...
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root_Gigi-3.counts
(6 total)
varLabels: sizeFactor condition countfiles
varMetadata: labelDescription
featureData
featureNames: Medtr0001s0010.1:E001 Medtr0001s0010.1:E002 ...
Medtr8g494250.1:E002 (228882 total)
fvarLabels: geneID exonID ... transcripts (13 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
>ecs.ConVsgigi.ESF <- estimateSizeFactors (ecs.ConVsgigi)
>head (counts(ecs.ConVsgigi.ESF), normalized=TRUE)
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root-1.counts
Medtr0001s0010.1:E001 0
Medtr0001s0010.1:E002 0
Medtr0001s0070.1:E001 0
Medtr0001s0100.1:E001 0
Medtr0001s0100.1:E002 0
Medtr0001s0120.1:E001 0
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root-2.counts
Medtr0001s0010.1:E001 0
Medtr0001s0010.1:E002 0
Medtr0001s0070.1:E001 0
Medtr0001s0100.1:E001 0
Medtr0001s0100.1:E002 0
Medtr0001s0120.1:E001 0
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root-3.counts
Medtr0001s0010.1:E001 0
Medtr0001s0010.1:E002 0
Medtr0001s0070.1:E001 0
Medtr0001s0100.1:E001 0
Medtr0001s0100.1:E002 0
Medtr0001s0120.1:E001 0
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root_Gigi-1.counts
Medtr0001s0010.1:E001 0
Medtr0001s0010.1:E002 0
Medtr0001s0070.1:E001 0
Medtr0001s0100.1:E001 0
Medtr0001s0100.1:E002 0
Medtr0001s0120.1:E001 0
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root_Gigi-2.counts
Medtr0001s0010.1:E001 0
Medtr0001s0010.1:E002 0
Medtr0001s0070.1:E001 0
Medtr0001s0100.1:E001 0
Medtr0001s0100.1:E002 0
Medtr0001s0120.1:E001 0
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root_Gigi-3.counts
Medtr0001s0010.1:E001 0
Medtr0001s0010.1:E002 0
Medtr0001s0070.1:E001 0
Medtr0001s0100.1:E001 0
Medtr0001s0100.1:E002 0
Medtr0001s0120.1:E001 0
>ecs.ConVsgigi.ED <- estimateDispersions (ecs.ConVsgigi.ESF, nCores=16)
............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
Done
>head (ecs.ConVsgigi.ED)
ExonCountSet (storageMode: environment)
assayData: 1 features, 6 samples
element names: counts
protocolData: none
phenoData
sampleNames:
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root-1.counts
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root-2.counts
...
/home/projects/medicago/mt_4.0_reference/Mt4.0v1/Annotation/DEXSeq/mt_root_Gigi-3.counts
(6 total)
varLabels: sizeFactor countfiles condition
varMetadata: labelDescription
featureData
featureNames: Medtr0001s0010.1:E001
fvarLabels: geneID exonID ... transcripts (13 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
>ecs.conVsgigi.FDF <- fitDispersionFunction (ecs.ConVsgigi.ED)
Error in fitDispersionFunction(ecs.ConVsgigi.ED) :
no CR dispersion estimations found, please first call
estimateDispersions function
=====================================================
Thanks
Anitha
On 7/29/14 2:34 PM, Simon Anders wrote:
> Please post the complete code, i.e., all the command that led up to
> the error message
>
> Simon
>
> On 29/07/14 22:31, Anitha Sundararajan wrote:
>> Hello-
>>
>> Has anyone seen the following error before with DEXSeq? I have run the
>> tool a couple times before with no issues.
>>
>> So when I try to run the "fitDispersionFunction", I get the following:
>>
>> *no CR dispersion estimations found, please first call
>> estimateDispersions function*
>>
>> I actually ran the estimateDispersions function prior to this without
>> any problem.
>>
>> Thanks so much for your help.
>> Anitha
>>
>> =====================================================
>> > 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] DEXSeq_1.8.0 Biobase_2.22.0 BiocGenerics_0.8.0
>> [4] BiocInstaller_1.12.1
>>
>> loaded via a namespace (and not attached):
>> [1] biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6
>> [4] GenomicRanges_1.14.4 hwriter_1.3 IRanges_1.20.7
>> [7] RCurl_1.95-4.1 Rsamtools_1.14.3 statmod_1.4.20
>> [10] stats4_3.0.2 stringr_0.6.2 tools_3.0.2
>> [13] XML_3.98-1.1 XVector_0.2.0 zlibbioc_1.8.0
>>
>>
>> [[alternative HTML version deleted]]
>>
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>
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