Added on 1st Aug: solved. Thank you everyone.
I was trying DEXSeq and I stuck at the dispersion estimation step.
I got exactly the same error as described in:
The process stuck there for hours and then threw out error messages as following:
1: In .local(object, ...) :
Exons with less than 11 counts will be discarded. For more details read the documentation, parameter minCount
2: In .local(object, ...) :
Genes with more than 70 testable exons will be kicked out of the analysis. For more details read the documentation, parameter maxExon
3: In .local(object, ...) :
Failed to set up model frames for genes ENSG (a bunch of gene names here)
I read the previous discussion where people mentioned by upgrade to Version 1.2.1 the problem will be solved. However, I downloaded the package this week so it is the newest version.
If anyone knows how to solve this problem, please kindly reply. I do appreciate it.
I have 3 replicates for both treatment and control, and the session information is attached below.
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-redhat-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
[7] base
other attached packages:
[1] pasilla_0.2.13 DESeq_1.8.3 locfit_1.5-9.1
[4] DEXSeq_1.2.1 Biobase_2.16.0 BiocGenerics_0.2.0
loaded via a namespace (and not attached):
[1] annotate_1.34.1 AnnotationDbi_1.18.4
[3] biomaRt_2.12.0 DBI_0.2-7
[5] genefilter_1.38.0 geneplotter_1.34.0
[7] grid_2.15.0 hwriter_1.3
[9] IRanges_1.14.4 lattice_0.20-6
[11] plyr_1.8 RColorBrewer_1.0-5
[13] RCurl_1.91-0 RSQLite_0.11.4
[15] splines_2.15.0 statmod_1.4.20
[17] stats4_2.15.0 stringr_0.5
[19] survival_2.36-12 tools_2.15.0
[21] XML_3.93-0 xtable_1.7-3
I was trying DEXSeq and I stuck at the dispersion estimation step.
I got exactly the same error as described in:
The process stuck there for hours and then threw out error messages as following:
1: In .local(object, ...) :
Exons with less than 11 counts will be discarded. For more details read the documentation, parameter minCount
2: In .local(object, ...) :
Genes with more than 70 testable exons will be kicked out of the analysis. For more details read the documentation, parameter maxExon
3: In .local(object, ...) :
Failed to set up model frames for genes ENSG (a bunch of gene names here)
I read the previous discussion where people mentioned by upgrade to Version 1.2.1 the problem will be solved. However, I downloaded the package this week so it is the newest version.
If anyone knows how to solve this problem, please kindly reply. I do appreciate it.
I have 3 replicates for both treatment and control, and the session information is attached below.
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-redhat-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
[7] base
other attached packages:
[1] pasilla_0.2.13 DESeq_1.8.3 locfit_1.5-9.1
[4] DEXSeq_1.2.1 Biobase_2.16.0 BiocGenerics_0.2.0
loaded via a namespace (and not attached):
[1] annotate_1.34.1 AnnotationDbi_1.18.4
[3] biomaRt_2.12.0 DBI_0.2-7
[5] genefilter_1.38.0 geneplotter_1.34.0
[7] grid_2.15.0 hwriter_1.3
[9] IRanges_1.14.4 lattice_0.20-6
[11] plyr_1.8 RColorBrewer_1.0-5
[13] RCurl_1.91-0 RSQLite_0.11.4
[15] splines_2.15.0 statmod_1.4.20
[17] stats4_2.15.0 stringr_0.5
[19] survival_2.36-12 tools_2.15.0
[21] XML_3.93-0 xtable_1.7-3
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