[BioC] Error DEXSeq

[Alejandro Reyes]

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") :
>   ‘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.
>
>
>