Hmm, looks like this is working to me. This is the typical DESeq startup, no errors.
You actually want to use R64. I really need to post some test data for folks to play around with. See below for an email I sent regarding some simulated RNA-Seq data that might be helpful.
-cheers, D
------ Forwarded Message
From: David Nix <dav...@hc...>
Date: Thu, 15 Jul 2010 08:53:32 -0600
To: Mariann Micsinai <mm...@ny...>, Jasreet Hundal <jh...@ge...>
Conversation: Overdispersed multiple replica RNA-Seq dataset
Subject: Overdispersed multiple replica RNA-Seq dataset
Hello Mariann and Jasreet,
It's been my intention to post another challenge to the Seqanswers forum but in this case just give the data and key and ask for submissions but I'm pretty much blown out of the water with analysis and programming requests and don't have time to put together the required documentation.
http://bioserver.hci.utah.edu/TempFiles/OverDispersedRNASeqDataset.zip
That said, this multiple replica overdispersed RNA-Seq dataset has proven quite helpful in sifting out which algorithms really work on more real world datasets.
I've posted the data (novoalignments which can be converted to SAM format if you prefer using the free Novocraft novo2sam.pl utility), the key, a bit of documentation as well as a some powerpoint slides detailing my work with the data.
If you use this data in a paper, please consider this a collaboration with the potential of authorship. It was a fair bit of work to put together, validate, and test this dataset.
-cheers, David
--
David Austin Nix, PhD | Bioinformatics Shared Resource | Huntsman Cancer Institute | 2000 Circle of Hope | SLC, UT 84112 | Rm: 3165 | Vc: 801.587.4611 | Fx: 801.585.6458 | dav...@hc... | Skype/iChat: LiveNix | WebSite: http://bioserver.hci.utah.edu | DAS/2: http://bioserver.hci.utah.edu:8080/DAS2DB/genome
On 7/26/10 11:42 PM, "M H" <mhd...@gm...> wrote:
Hi,
I have installed all the dependencies but still I am getting the following error.
> library(DESeq)
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: locfit
Loading required package: akima
Loading required package: lattice
locfit 1.5-6 2010-01-20
Is there any problem with R64 or how can this be figured out to start functioning. Your help in this regard will highly be appreciated.
M. Hussain
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