[BioC] Error DEXSeq
Mallon, Eamonn B. (Dr.)
ebm3 at leicester.ac.uk
Thu May 22 12:01:31 CEST 2014
Hi Alejandro,
I was having a similar problem. I finished the analysis earlier in the
year (on an earlier version of DEXSeq) but now would like to draw some of
the pictures separately. I tried to run the analysis again. I¹ve changed
to DEXSeqDataSeqFromHTSeq and now have the error
Error in .local(x, ...) : strand values must be in '+' '-' Œ*'
I guess this means something is now wrong with my GFF file.
Its first line looks like
gi|313870964|gb|AELG01010669.1| dexseq_prepare_annotation.py aggregate_gene
2 1088 . . . gene_id "XLOC_000001"
Any help would be appreciated.
Eamonn
Dr Eamonn Mallon
Lecturer in Evolutionary Biology
Adrian 220
Biology Department
University of Leicester
http://www2.le.ac.uk/departments/biology/people/mallon
On 22/05/2014 10:53, "Alejandro Reyes" <alejandro.reyes at embl.de> wrote:
>Hi Roberta,
>
>Yes, the newer versions of DEXSeq have lots of updates, in the new
>vignette
>you will the description of the new functions. As the error message
>indicates,
>some functions were deprecated and substituted for new ones, including the
>functions that created the objects. In your case, you need to use
>DEXSeqDataSeqFromHTSeq instead of read.HTSeqCounts.
>
>Let me know if it works!
>Best regards,
>Alejandro
>
>ps. I think we might have more efficient/effective communication if we
>keep the e-mails concerning
>the same issue in the same thread, rather than double posting and having
>many parallel
>conversations: I have cc-ed Simon in this e-mail :)
>
>
>
>> Hi Alejandro,
>> I updated to the current release versione of DEXSeq as you can see.
>>
>> sessionInfo()
>> R version 3.1.0 (2014-04-10)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>
>> locale:
>> [1] it_IT.UTF-8/it_IT.UTF-8/it_IT.UTF-8/C/it_IT.UTF-8/it_IT.UTF-8
>>
>> attached base packages:
>> [1] parallel stats graphics grDevices utils datasets
>> methods base
>>
>> other attached packages:
>> [1] DEXSeq_1.10.3 BiocParallel_0.6.0 DESeq2_1.4.5
>> RcppArmadillo_0.4.300.0 Rcpp_0.11.1
>> GenomicRanges_1.16.3 GenomeInfoDb_1.0.2 IRanges_1.22.6
>> Biobase_2.24.0
>> [10] BiocGenerics_0.10.0 BiocInstaller_1.14.2
>>
>> loaded via a namespace (and not attached):
>> [1] annotate_1.42.0 AnnotationDbi_1.26.0 BatchJobs_1.2
>> BBmisc_1.6 biomaRt_2.20.0 Biostrings_2.32.0
>> bitops_1.0-6 brew_1.0-6 codetools_0.2-8
>> DBI_0.2-7 digest_0.6.4
>> [12] fail_1.2 foreach_1.4.2 genefilter_1.46.1
>> geneplotter_1.42.0 grid_3.1.0 hwriter_1.3
>> iterators_1.0.7 lattice_0.20-29 locfit_1.5-9.1
>> plyr_1.8.1 RColorBrewer_1.0-5
>> [23] RCurl_1.95-4.1 Rsamtools_1.16.0 RSQLite_0.11.4
>> sendmailR_1.1-2 splines_3.1.0 statmod_1.4.19
>> stats4_3.1.0 stringr_0.6.2 survival_2.37-7
>> tools_3.1.0 XML_3.98-1.1
>> [34] xtable_1.7-3 XVector_0.4.0 zlibbioc_1.10.0
>>
>> Now I have another error message in the previous steps:
>>
>> ecs <- read.HTSeqCounts (sampleTable$countFile, sampleTable ,
>> "genes.gff")
>> Errore in checkAtAssignment("character", "annotationFile", "character")
>>:
>> ŒannotationFile¹ is not a slot in class ³character²
>> Inoltre: Warning message:
>> 'newExonCountSet' is deprecated.
>> Use 'DEXSeqDataSet' instead.
>> See help("Deprecated")
>>
>> How can I solve it?
>>
>> Thank you
>>
>>
>> Alejandro Reyes <alejandro.reyes at embl.de> ha scritto:
>>
>>> Dear Carriero,
>>>
>>> I think you forgot to copy the output of your sessionInfo()?
>>>
>>> I think you might be using a very old version of DEXSeq. If so, could
>>> you please update at least to the current release version of DEXSeq
>>> (1.10.3), try again and write back if it keeps giving you error
>>> messages?
>>>
>>> Best regards,
>>> Alejandro
>>>
>>>> I have a warning message when I estimate the dipersion parameter. I
>>>> can't carry on because of some other error messages in the following
>>>> steps, as I attached below.
>>>> Thanks in advance
>>>>
>>>> -- output of sessionInfo():
>>>>
>>>> sizeFactors (ecs)
>>>> 7A31.counts 7A32.counts 7A33.counts 46BR1.counts 46BR2.counts
>>>> 46BR3.counts
>>>> 1.0177858 1.0753635 1.1738656 0.9085247 0.9827212
>>>> 0.9198726
>>>>> ecs<- estimateDispersions ( ecs )
>>>> Dispersion estimation. (Progress report: one dot per 100 genes)
>>>>
>>>>.......................................................................
>>>>............................................................
>>>>
>>>> Warning messages:
>>>> 1: In .local(object, ...) :
>>>> Exons with less than 11 counts will be discarded. For more details
>>>> read the documentation, parameter minCount
>>>> 2: In .local(object, ...) :
>>>> Genes with more than 70 testable exons will be kicked out of the
>>>> analysis. For more details read the documentation, parameter maxExon
>>>>> ecs <- fitDispersionFunction(ecs)
>>>> Error in if (sum(log(coefs/oldcoefs)^2) < 0.005) break :
>>>> missing value where TRUE/FALSE needed
>>>> In addition: Warning messages:
>>>> 1: In glmgam.fit(mm, disps[good], start = coefs) :
>>>> Too much damping - convergence tolerance not achievable
>>>> 2: In log(coefs/oldcoefs) : NaNs produced
>>>>> head( fData (ecs)$dispBeforeSharing)
>>>> [1] 0.000000e+00 6.003931e-03 4.852941e-03 0.000000e+00 2.771527e-10
>>>> [6] 0.000000e+00
>>>>> ecs at dispFitCoefs
>>>> [1] NA NA
>>>>> head(fData(ecs)$dispFitted)
>>>> [1] NA NA NA NA NA NA
>>>>> plotDispEsts(ecs)
>>>> Error: could not find function "plotDispEsts"
>>>>> ecs<-testForDEU(ecs)
>>>> Error in testForDEU(ecs) :
>>>> No dispersion values found, call function fitDispersionFunction
>>>> first.
>>>>
>>>> --
>>>> Sent via the guest posting facility at bioconductor.org.
>>
>>
>>
>
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