DESeq upgrade

[fatakias]

Dear R experts and / or DESeq expert(s),

I am using DESeq v1.8.2 and would like to upgrade. The current version available is v1.9.4.

From an R session, I am using the update.packages() command .. (please see below for details), but it does not work.

Q1- Can you please suggest a fix. Which R command / series of commands would work?
Q2 - Would this be a general fix for upgrading to other such R packages, such as edgeR.

Thanks in advance.
Best,
sarosh

> require(DESeq);
> sessionInfo();


R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] BiocInstaller_1.4.4 DESeq_1.8.2         locfit_1.5-8
[4] Biobase_2.16.0      BiocGenerics_0.2.0

loaded via a namespace (and not attached):
 [1] annotate_1.34.0      AnnotationDbi_1.18.0 DBI_0.2-5
 [4] genefilter_1.38.0    geneplotter_1.34.0   grid_2.15.0
 [7] IRanges_1.14.2       lattice_0.20-6       RColorBrewer_1.0-5
[10] RSQLite_0.11.1       splines_2.15.0       stats4_2.15.0
[13] survival_2.36-14     tcltk_2.15.0         tools_2.15.0
[16] xtable_1.7-0
>
--------------------------------------------------------------

> update.packages("DESeq");
>

--------------------------------------------------------------
--------------------------------------------------------------
> sessionInfo();
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] BiocInstaller_1.4.4 DESeq_1.8.2         locfit_1.5-8
[4] Biobase_2.16.0      BiocGenerics_0.2.0

loaded via a namespace (and not attached):
 [1] annotate_1.34.0      AnnotationDbi_1.18.0 DBI_0.2-5
 [4] genefilter_1.38.0    geneplotter_1.34.0   grid_2.15.0
 [7] IRanges_1.14.2       lattice_0.20-6       RColorBrewer_1.0-5
[10] RSQLite_0.11.1       splines_2.15.0       stats4_2.15.0
[13] survival_2.36-14     tcltk_2.15.0         tools_2.15.0
[16] xtable_1.7-0

--------------------------------------------------------------

[ramouz87]

Hi
run the following to update all existing bioconductor packages:

source("http://bioconductor.org/biocLite.R")
pkgs <- rownames(installed.packages())
biocLite(pkgs)

Best,
Ramzi

[fatakias]

Thanks Ramzi,
The DESeq version remains unchanged at 1.8.2. This is the sessionInfo() output after the command is run in an R session. It seems to me that other packages retain the previous version (compare with that in previous post)... does not mean that all versions are new and need updates though. I am aware DESeq has a new version and that is not updated in an R session. Maybe this is not the way to update .. hope other experts can please help.
Best,
sarosh

> sessionInfo();
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] edgeR_2.6.1         limma_3.12.0        DESeq_1.8.2        
[4] locfit_1.5-8        Biobase_2.16.0      BiocGenerics_0.2.0 
[7] BiocInstaller_1.4.4

loaded via a namespace (and not attached):
 [1] annotate_1.34.0      AnnotationDbi_1.18.0 DBI_0.2-5           
 [4] genefilter_1.38.0    geneplotter_1.34.0   grid_2.15.0         
 [7] IRanges_1.14.2       lattice_0.20-6       RColorBrewer_1.0-5  
[10] RSQLite_0.11.1       splines_2.15.0       stats4_2.15.0       
[13] survival_2.36-14     tools_2.15.0         xtable_1.7-0        
>

[arvid]

The latest stable version of DESeq is v1.8.2, which is the current version in Bioconductor 2.10 for R 2.15. So everything is working as expected for your setup.
DESeq 1.9.4 is a development (and thus unstable) version, which you can install from the Bioconductor devel version, under the R devel version. See "Installing packages from the development repository" in http://www.bioconductor.org/help/faq...l-packages-faq...

[HvDeut]

I tried to update DESeq and DEXSeq using:

source("http://bioconductor.org/biocLite.R")
pkgs <- rownames(installed.packages())
biocLite(pkgs)

but my packages remain the older ones.

My question now is, how do I go from DEXSeq 1.6.0 to 1.8.0 ??

[bruce01]

To update DEXseq to current version, follow instructions from: this page

If you cannot update it may be that you are not able to connect to internet through your R. Test via: this page