[BioC] DEXSeq- fitDispersionFunction error

[Rao,Xiayu]

This is a previous post that solved my problem, which might also help you.

Best,
Xiayu
 

-----Original Message-----
From: Alejandro Reyes [mailto:alejandro.reyes at embl.de] 
Sent: Tuesday, April 22, 2014 11:33 AM
To: Rao,Xiayu; 'bioconductor at r-project.org'
Subject: Re: dexseq fitDispersionFunction(ecs) error

Dear Xiayu,

Thanks for your report, we are looking into that right now, it has to do with versions of dependencies outside bioconductor.

As a temporary solution, you can install an old version of statmod compatible with your version of DEXSeq by doing in your R session:

library(devtools);install_url("http://cran.r-project.org/src/contrib/Archive/statmod/statmod_1.4.18.tar.gz")

Your code below should work then!

Best regards,
Alejandro







-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Anitha Sundararajan
Sent: Tuesday, July 29, 2014 3:32 PM
To: bioconductor at r-project.org; bioconductor at stat.math.ethz.ch
Subject: [BioC] DEXSeq- fitDispersionFunction error

Hello-

Has anyone seen the following error before with DEXSeq?  I have run the tool a couple times before with no issues.

So when I try to run the "fitDispersionFunction", I get the following:

*no CR dispersion estimations found, please first call estimateDispersions function*

I actually ran the estimateDispersions function prior to this without any problem.

Thanks so much for your help.
Anitha

=====================================================
 > sessionInfo()
R version 3.0.2 (2013-09-25)
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=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets methods
[8] base

other attached packages:
[1] DEXSeq_1.8.0         Biobase_2.22.0       BiocGenerics_0.8.0
[4] BiocInstaller_1.12.1

loaded via a namespace (and not attached):
  [1] biomaRt_2.18.0       Biostrings_2.30.1    bitops_1.0-6
  [4] GenomicRanges_1.14.4 hwriter_1.3          IRanges_1.20.7
  [7] RCurl_1.95-4.1       Rsamtools_1.14.3     statmod_1.4.20
[10] stats4_3.0.2         stringr_0.6.2        tools_3.0.2
[13] XML_3.98-1.1         XVector_0.2.0        zlibbioc_1.8.0


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