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Old 12-06-2011, 05:33 AM   #1
RockChalkJayhawk
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Location: Rochester, MN

Join Date: Mar 2009
Posts: 191
Default glmnb.fit in DEXSeq

Does anyone else have this problem?
Code:
library(DEXSeq)
annotationfile = file.path("/TN_RNA-Seq/Alt_SPlicing/DEXSeq/hg19.prepared.gtf")
samples=read.table("Targets/Samples.txt",row.names=1)
inDir=file.path("/TN_RNA-Seq/Alt_SPlicing/DEXSeq/Targets")

ecs = read.HTSeqCounts(countfiles = file.path(inDir, paste(rownames(samples))),design = samples,flattenedfile = annotationfile)

ecs <- makeCompleteDEUAnalysis(ecs)
Dispersion estimation. (Progress report: one dot per 100 genes)
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
In addition: Warning message:
In .local(object, ...) :
  Exons with less than 11 counts will be discarded. For more details read the documentation, parameter minCount
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"
Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) :
  could not find function "glmnb.fit"

Error in fitDispersionFunction(ecs) :
  no CR dispersion estimations found, please first call estimateDispersions function
In addition: There were 22 warnings (use warnings() to see them)
or else does anyone know what the function glmnb.fit is supposed to be?

I updated my statmod library, but I don't see the function.
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Old 12-06-2011, 07:09 AM   #2
Simon Anders
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Could you please post the output of 'sessionInfo()'?

As you correctly noticed, 'glmnb.fit' comes with 'statmod' and at least in the current version, 1.4.14, it is available.
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Old 12-06-2011, 07:11 AM   #3
RockChalkJayhawk
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Location: Rochester, MN

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Code:
> sessionInfo()
R version 2.12.0 (2010-10-15)
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=C              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] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] stringr_0.5    statmod_1.4.6  MASS_7.3-8     pasilla_0.2.10 DEXSeq_1.0.1
[6] Biobase_2.14.0

loaded via a namespace (and not attached):
[1] hwriter_1.3  plyr_1.6     tools_2.12.0
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Old 12-06-2011, 07:17 AM   #4
Simon Anders
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The current version of statmod is 1.4.14 but you have 1.4.6. This is your problem.

If you install Bioconductor packages, please use the biocLite script as explained here. However, note that Bioconductor versions are tied to R versions: If you use R 2.12, you will get packages from Bioconductor 2.7. DEXSeq is only available since the current Bioconductor release, Bioconductor 2.9, which biocLite will only use if you have the current R version, namely R 2.14.
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Old 12-06-2011, 07:18 AM   #5
RockChalkJayhawk
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Got it Simon. I'll post just to make sure this takes care of it.
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Old 12-06-2011, 07:29 AM   #6
RockChalkJayhawk
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That did it. Thanks again.
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