Hello all,

I am having problem with the DEXseq program using TRT functions, 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.
As mentioned in earlier discussion, I have sourced the TRT functions from
the svn repository, and successfully completed the
estimateDispersionsTRT. However, I ran into this error when running
fitDispersionFunction:

Am I doing something wrong?

Thanks for the help

Uma

> ecs.p = fitDispersikonFunction(ecs.p)
Error: could not find function "fitDispersikonFunction"
> ecs.p = fitDispersionFunction(ecs.p)
Error in glmgam.fit(mm, disps[good], start = coefs) :
  unused argument (start = coefs)
Error in fitDispersionFunction(ecs.p) :
  Failed to fit the dispersion function
 > 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 statmod_1.4.18

loaded via a namespace (and not attached):
 [1] annotate_1.40.0         AnnotationDbi_1.24.0    biomaRt_2.18.0
 [4] Biostrings_2.30.1       bitops_1.0-6            DBI_0.2-7
 [7] DESeq_1.14.0            DESeq2_1.2.5            genefilter_1.44.0
[10] geneplotter_1.40.0      GenomicRanges_1.14.3    grid_3.0.2
[13] hwriter_1.3             IRanges_1.20.6          lattice_0.20-24
[16] locfit_1.5-9.1          RColorBrewer_1.0-5      Rcpp_0.10.6
[19] RcppArmadillo_0.3.920.3 RCurl_1.95-4.1          Rsamtools_1.14.2
[22] RSQLite_0.11.4          splines_3.0.2           stats4_3.0.2
[25] stringr_0.6.2           survival_2.37-4         XML_3.98-1.1
[28] xtable_1.7-1            XVector_0.2.0           zlibbioc_1.8.0

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