[BioC] DEXseq: fitDispersionFunction error

Alejandro Reyes alejandro.reyes at embl.de
Fri Feb 17 16:15:49 CET 2012


Dear Elena,

You can always use the svn to get the latests versions:
http://www.bioconductor.org/developers/source-control/

Bests,
Alejandro



> Dear Alejandro,
>
> I can't seem to find the development version that you were talking 
> about. I am running the version available for BioC 2.9: 
> http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq.html
>
> ...Could you tell me where to download v 1.1.6 of your software?
>
> Thanks,
> Elena
>
> On 2/17/2012 6:11 AM, Alejandro Reyes wrote:
>> Dear Elena,
>>
>> I am glad you like the package!
>> We recently fixed this bug, it should be fine if you use the most 
>> recent development
>> version of DEXSeq (1.1.6)
>>
>> This should be solved by then, if not, could you send me your ecs 
>> object to give it a
>> closer look?
>>
>> Thanks!
>>
>> Alejandro
>>
>>
>> Greetings all,
>>
>> I ran into another problem with the DEXseq program, and I was hoping
>> that somebody could help me once more.  I successfully ran through a
>> full analysis of one time point of my dataset, and was hoping ideally to
>> extend the analysis to my full time course, using the GLM test. However,
>> I ran into this error when running fitDispersionFunction:
>>
>> >  ecs<- fitDispersionFunction(ecs)
>> Warning messages:
>> 1: In glmgam.fit(mm, disps[good], start = coefs) :
>>    Too much damping - convergence tolerance not achievable
>> 2: In glmgam.fit(mm, disps[good], start = coefs) :
>>    Too much damping - convergence tolerance not achievable
>>
>> I couldn't find the answer in the list archive. Do the DEXseq authors or
>> anyone else know what this error means?
>>
>> I'd be truly grateful for any advice about this - I really like the
>> DEXseq package, and I'm hoping to use/reference it in my manuscript if I
>> can get it to work!  My full script is below.
>>
>> Sincerely,
>> Elena
>> -------------------------------------
>> >  library(DEXSeq)
>> >  annotationfile = file.path("../DEXSeq_annotations.gff")
>> >  annotationfile
>> [1] "../DEXSeq_annotations.gff"
>> >  samples<- read.table("PLdesign.txt",header=T,row.names=1)
>> >  samples
>>            treatment time
>> PL_D1hr_1   vehicle  one
>> PL_D1hr_2   vehicle  one
>> PL_U1hr_1      drug  one
>> PL_U1hr_2      drug  one
>> PL_D2hr_1   vehicle  two
>> PL_D2hr_2   vehicle  two
>> PL_U2hr_1      drug  two
>> PL_U2hr_2      drug  two
>> PL_D4hr_1   vehicle four
>> PL_D4hr_2   vehicle four
>> PL_U4hr_1      drug four
>> PL_U4hr_2      drug four
>> PL_D6hr_1   vehicle  six
>> PL_D6hr_2   vehicle  six
>> PL_U6hr_1      drug  six
>> PL_U6hr_2      drug  six
>> >  fullFilenames<- list.files(full.names=TRUE,pattern="exon.txt")
>> >  fullFilenames
>>   [1] "./PL_1hrD1_exon.txt" "./PL_1hrD2_exon.txt" "./PL_1hrU1_exon.txt"
>>   [4] "./PL_1hrU2_exon.txt" "./PL_2hrD1_exon.txt" "./PL_2hrD2_exon.txt"
>>   [7] "./PL_2hrU1_exon.txt" "./PL_2hrU2_exon.txt" "./PL_4hrD1_exon.txt"
>> [10] "./PL_4hrD2_exon.txt" "./PL_4hrU1_exon.txt" "./PL_4hrU2_exon.txt"
>> [13] "./PL_6hrD1_exon.txt" "./PL_6hrD2_exon.txt" "./PL_6hrU1_exon.txt"
>> [16] "./PL_6hrU2_exon.txt"
>> >  ecs<- read.HTSeqCounts(countfiles = fullFilenames,design =
>> samples,flattenedfile = annotationfile)
>> # Check out ecs object
>> >  head(counts(ecs))
>>             ./PL_1hrD1_exon.txt ./PL_1hrD2_exon.txt ./PL_1hrU1_exon.txt
>> 2L52.1:001                  12                  16                   7
>> 2L52.1:002                  32                  22                  19
>> 2L52.1:003                  18                  16                  14
>> 2L52.1:004                  19                  16                  20
>> 2L52.1:005                  28                  22                   9
>> 2L52.1:006                  19                  15                  22
>>             ./PL_1hrU2_exon.txt ./PL_2hrD1_exon.txt ./PL_2hrD2_exon.txt
>> 2L52.1:001                   4                   7                   4
>> 2L52.1:002                  19                  23                  16
>> 2L52.1:003                  20                  15                  17
>> 2L52.1:004                  11                   8                  17
>> 2L52.1:005                  17                  23                  27
>> 2L52.1:006                  20                  19                  23
>>             ./PL_2hrU1_exon.txt ./PL_2hrU2_exon.txt ./PL_4hrD1_exon.txt
>> 2L52.1:001                   2                   4                   0
>> 2L52.1:002                  18                  13                  13
>> 2L52.1:003                  15                   5                  15
>> 2L52.1:004                  12                   4                   8
>> 2L52.1:005                  18                  14                  13
>> 2L52.1:006                  15                  10                  13
>>             ./PL_4hrD2_exon.txt ./PL_4hrU1_exon.txt ./PL_4hrU2_exon.txt
>> 2L52.1:001                   2                   1                   1
>> 2L52.1:002                   9                   6                   8
>> 2L52.1:003                   5                   3                  17
>> 2L52.1:004                   2                   3                   7
>> 2L52.1:005                  17                   4                   5
>> 2L52.1:006                  16                   4                   6
>>             ./PL_6hrD1_exon.txt ./PL_6hrD2_exon.txt ./PL_6hrU1_exon.txt
>> 2L52.1:001                   4                   2                   0
>> 2L52.1:002                  20                  13                   4
>> 2L52.1:003                   8                   7                   7
>> 2L52.1:004                   7                   4                   6
>> 2L52.1:005                  14                  16                   9
>> 2L52.1:006                  12                  13                   6
>>             ./PL_6hrU2_exon.txt
>> 2L52.1:001                   2
>> 2L52.1:002                  12
>> 2L52.1:003                   8
>> 2L52.1:004                   4
>> 2L52.1:005                   6
>> 2L52.1:006                   4
>> >  design(ecs)
>>                      treatment time
>> ./PL_1hrD1_exon.txt   vehicle  one
>> ./PL_1hrD2_exon.txt   vehicle  one
>> ./PL_1hrU1_exon.txt      drug  one
>> ./PL_1hrU2_exon.txt      drug  one
>> ./PL_2hrD1_exon.txt   vehicle  two
>> ./PL_2hrD2_exon.txt   vehicle  two
>> ./PL_2hrU1_exon.txt      drug  two
>> ./PL_2hrU2_exon.txt      drug  two
>> ./PL_4hrD1_exon.txt   vehicle four
>> ./PL_4hrD2_exon.txt   vehicle four
>> ./PL_4hrU1_exon.txt      drug four
>> ./PL_4hrU2_exon.txt      drug four
>> ./PL_6hrD1_exon.txt   vehicle  six
>> ./PL_6hrD2_exon.txt   vehicle  six
>> ./PL_6hrU1_exon.txt      drug  six
>> ./PL_6hrU2_exon.txt      drug  six
>> >  head(fData(ecs))
>>             geneID exonID testable dispBeforeSharing dispFitted 
>> dispersion
>> 2L52.1:001 2L52.1   E001       NA                NA         
>> NA         NA
>> 2L52.1:002 2L52.1   E002       NA                NA         
>> NA         NA
>> 2L52.1:003 2L52.1   E003       NA                NA         
>> NA         NA
>> 2L52.1:004 2L52.1   E004       NA                NA         
>> NA         NA
>> 2L52.1:005 2L52.1   E005       NA                NA         
>> NA         NA
>> 2L52.1:006 2L52.1   E006       NA                NA         
>> NA         NA
>>             pvalue padjust   chr start  end strand transcripts
>> 2L52.1:001     NA      NA chrII  1867 1911      +      2L52.1
>> 2L52.1:002     NA      NA chrII  2506 2694      +      2L52.1
>> 2L52.1:003     NA      NA chrII  2738 2888      +      2L52.1
>> 2L52.1:004     NA      NA chrII  2931 3036      +      2L52.1
>> 2L52.1:005     NA      NA chrII  3406 3552      +      2L52.1
>> 2L52.1:006     NA      NA chrII  3802 3984      +      2L52.1
>> # All in all, Exon Count Set looks good
>> >  ecs<- estimateSizeFactors(ecs)
>> >  sizeFactors(ecs)
>> ./PL_1hrD1_exon.txt ./PL_1hrD2_exon.txt ./PL_1hrU1_exon.txt
>> ./PL_1hrU2_exon.txt
>>            1.7543472           1.6354950           1.6969669
>> 1.5496025
>> ./PL_2hrD1_exon.txt ./PL_2hrD2_exon.txt ./PL_2hrU1_exon.txt
>> ./PL_2hrU2_exon.txt
>>            1.4932349           1.3392481           1.4051111
>> 1.1780430
>> ./PL_4hrD1_exon.txt ./PL_4hrD2_exon.txt ./PL_4hrU1_exon.txt
>> ./PL_4hrU2_exon.txt
>>            0.9026051           0.5879963           0.5206059
>> 0.5726255
>> ./PL_6hrD1_exon.txt ./PL_6hrD2_exon.txt ./PL_6hrU1_exon.txt
>> ./PL_6hrU2_exon.txt
>>            0.7345296           0.7536120           0.7763199
>> 0.7529934
>> >  formuladispersion<- count ~ sample + ( exon + treatment ) * time
>> >  ecs<- estimateDispersions( ecs, formula = formuladispersion, 
>> nCores=11)
>> Estimating Cox-Reid exon dispersion estimates using 11 cores. (Progress
>> report: one dot per 100 genes)
>> ..........................................................................................................................................................> 
>>
>>
>> >  /usr/local/lib64/R/library
>> >  ecs<- fitDispersionFunction(ecs)
>> Warning messages:
>> 1: In glmgam.fit(mm, disps[good], start = coefs) :
>>    Too much damping - convergence tolerance not achievable
>> 2: In glmgam.fit(mm, disps[good], start = coefs) :
>>    Too much damping - convergence tolerance not achievable
>>
>> >  sessionInfo()
>> R version 2.14.0 (2011-10-31)
>> 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=C                 LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] multicore_0.1-7 DEXSeq_1.0.2    Biobase_2.14.0
>>
>> loaded via a namespace (and not attached):
>> [1] hwriter_1.3    plyr_1.7.1     statmod_1.4.14 stringr_0.6
>> tools_2.14.0
>> >
>>
>



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