I had the similar problems as you and figured it out by using the old version manual (2010-01-19) with R2.11.1. Forget the "normalized" and " estimateDispersions" now
Maybe somebody can use both to get the correct results (I cannot). And it will be great if s/he can share her/his details/experience with using "normalized" and " estimateDispersions" .
In addition, I am using R2.13.2 and cannot even successfully install the latest DESeq, Could anybody give my some ideas? Thanks.
> library("DESeq")
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
Loading required package: locfit
Loading required package: akima
locfit 1.5-6 2010-01-20
Error in library.dynam(lib, package, package.lib) :
DLL 'genefilter' not found: maybe not installed for this architecture?
In addition: Warning messages:
1: '.readRDS' is deprecated.
Use 'readRDS' instead.
See help("Deprecated")
2: '.readRDS' is deprecated.
Use 'readRDS' instead.
See help("Deprecated")
Error: package/namespace load failed for 'DESeq'
Quote:
Originally Posted by janec
I'm running DESeq for the first time and am having a few problems. I'm working through the documentation dated August 11, 2011.
I had no problems setting up a CountDataSet object with my counts table and can access the counts and estimate size factors for samples fine.
However when I tried to call the normalised counts, using the "normalized = TRUE" argument for the counts accessor, it says that there's no argument with that name. When I look at the man page for "counts", it also appears to have no arguments other than the name of the object it is counting.
I skipped that step and went on to the variance estimation stage, but when I try to run the estimateDispersions function I get a "function not found" message.
Is there something else I need to have installed?
Cheers!
|