[BioC] error in DEXSeq fitDispersionFunction()

Wolfgang Huber whuber at embl.de
Mon Dec 5 22:40:15 CET 2011


Dear Georg

thank you for your feedback. I am afraid you have found a bug. I have 
contacted you privately (outside this list), ideally we can use your 
dataset in order to troubleshoot and fix this.

	Thank you and best wishes
	Wolfgang


On 12/5/11 8:03 PM, Georg Otto wrote:
> Wolfgang Huber<whuber at embl.de>  writes:
>
> Dear Wolfgang,
>
> thanks for your help. I tried with version 1.1.1 and still got the same
> message:
>
> 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
>
> Apparently in the function fitDispersionFunction(), the expression
>
> sum(log(coefs/oldcoefs)^2)
>
> produces NAs with my data, so
>
> if (sum(log(coefs/oldcoefs)^2)<  0.005)
>
> gives an error... any idea, how to fix this?
>
> Cheers,
>
> Georg
>
>
>> Dear Georg
>>
>> Thank you. Can you please try with a more recent version of DEXSeq,
>> e.g. 1.1.1 from the last release? The package has changed a lot since
>> 1.0.1, including in places that appear relevant to your problem.
>>
>> 	Best wishes
>> 	Wolfgang
>>
>> 	
>>
>> On 11/29/11 3:30 PM, Georg Otto wrote:
>>> Dear Bioconductors,
>>>
>>>
>>> I am trying to use DEXSeq to test for differential exon usage in my
>>> RNA-seq data. I was able to generate the exon count tables using the
>>> python scripts that come with the package and the function
>>> read.HTSeqCounts(). However, I get an error at this step:
>>>
>>> exon.counts<- fitDispersionFunction(exon.counts)
>>>
>>>    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
>>>
>>> Any idea what might be wrong here?
>>>
>>> Here is the output of sessionInfo()
>>>
>>>
>>> R version 2.13.0 (2011-04-13)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>
>>> locale:
>>>    [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>>>    [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>>>    [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8
>>>    [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>>>    [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] DEXSeq_1.0.1          DESeq_1.6.1           locfit_1.5-6
>>> [4] lattice_0.19-26       akima_0.5-4           Biobase_2.14.0
>>> [7] GenomicFeatures_1.4.4 GenomicRanges_1.4.8   IRanges_1.10.6
>>>
>>> loaded via a namespace (and not attached):
>>>    [1] annotate_1.30.0      AnnotationDbi_1.14.1 biomaRt_2.8.1
>>>    [4] Biostrings_2.20.1    BSgenome_1.20.0      DBI_0.2-5
>>>    [7] genefilter_1.34.0    geneplotter_1.30.0   grid_2.13.0
>>> [10] hwriter_1.3          plyr_1.6             RColorBrewer_1.0-2
>>> [13] RCurl_1.7-0          RSQLite_0.10.0       rtracklayer_1.12.4
>>> [16] splines_2.13.0       statmod_1.4.14       stringr_0.5
>>> [19] survival_2.36-9      tools_2.13.0         XML_3.4-3
>>> [22] xtable_1.6-0
>>>
>>>
>>>
>>> Cheers,
>>>
>>> Georg
>>>
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>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber



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