1.) On a fresh install of R 2.13.2 (Win 7), I am trying to install the current version of DESeq from http://bioconductor.org/packages/dev...tml/DESeq.html.
According to that page, the version to be installed should be version 1.5.35.
However when I install it with these commands:
source("http://bioconductor.org/biocLite.R")
biocLite("DESeq")
and then check the installed version (installed.packages()[,c("Package","Version")]) I get:
DESeq "DESeq" "1.4.1"
2.) In the manual I noticed that there seems to be a new function, called "estimateDispersions" which seems to be similar to what was previously "estimateVarianceFunctions". I am referring to the manual PDF dated "October 29, 2011". However this new function does not seem to exist in my installation (this could be related to the above point of it being version 1.4.1):
> cds <- estimateDispersions(cds, method="blind", sharingMode="fit-only")
Error: could not find function "estimateDispersions"
3.) I have written a couple of scripts that contain calls to "estimateVarianceFunctions" - will they still work with future versions of DESeq?
4.) One thing I noted about the conds vector. Prevously (manual from "April 21, 2011") it was defined like this:
conds <- c( "T", "T", "T", "Tb", "N", "N" )
But now it's defined like this:
conds <- factor( c( "treated", "treated", "untreated", "untreated" ) )
So previously it was a vector and now it is a factor. Again, I wonder if old scripts need to be changed?
According to that page, the version to be installed should be version 1.5.35.
However when I install it with these commands:
source("http://bioconductor.org/biocLite.R")
biocLite("DESeq")
and then check the installed version (installed.packages()[,c("Package","Version")]) I get:
DESeq "DESeq" "1.4.1"
2.) In the manual I noticed that there seems to be a new function, called "estimateDispersions" which seems to be similar to what was previously "estimateVarianceFunctions". I am referring to the manual PDF dated "October 29, 2011". However this new function does not seem to exist in my installation (this could be related to the above point of it being version 1.4.1):
> cds <- estimateDispersions(cds, method="blind", sharingMode="fit-only")
Error: could not find function "estimateDispersions"
3.) I have written a couple of scripts that contain calls to "estimateVarianceFunctions" - will they still work with future versions of DESeq?
4.) One thing I noted about the conds vector. Prevously (manual from "April 21, 2011") it was defined like this:
conds <- c( "T", "T", "T", "Tb", "N", "N" )
But now it's defined like this:
conds <- factor( c( "treated", "treated", "untreated", "untreated" ) )
So previously it was a vector and now it is a factor. Again, I wonder if old scripts need to be changed?
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