[BioC] Error DEXSeq

[Roberta Carriero]

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") :
   ‘annotationFile’ is not a slot in class “character”
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.