[BioC] RnaSeqTutorial Package

[Steve Lianoglou]

Hi,

On Tue, Jun 19, 2012 at 5:20 PM, spf385 [guest] <guest at bioconductor.org> wrote:
>
> Greetings,
>
> I'm working my way through the tutorials for several RNA-Seq packages in R / bioconductor (EdgeR, DESeq, DEXSeq, ShortReads, etc.); and I've somewhat backed up to using the package RnaSeqTutorial (EBI, October 2011; Nicolas Delhomme).
>
> As I work my way through the documentation I stumble at section 2.3 Loading the annotation.
>
> it provides,
>
>> library(BSgenome.Dmelanogaster.UCSC.dm3)
>
> and I get the error message: Error in library(BSgenome.Dmelanogaster.UCSC.dm3); there is no package called 'BSgenome.Dmelanogaster.UCSC.dm3'

You have to install this package as it is not installed by default. For example:

R> source("http://bioconductor.org/biocLite.R")
R> biocLite("BSgenome.Dmelanogaster.UCSC.dm3")

> is the above a typo? and should it read something to the effect of
>
>>library(BSgenome)
>
>>Dmelano <- data(Dmelanogaster.UCSC.dm3, package = "BSgenome")
>
>
> Or is it that BSgenome is built under a different version of R? I have downloaded the source package and can locate said "Dmelanogaster.UCSC.dm3-seed"

Please don't take this the wrong way, but it seems as like you're
still a bit shaky with using R. I'd strongly recommend getting a
better handle on R basics before diving into any type of more advanced
analysis (like the tutorials you are reading through).

The investment of time in the basics will more than make up for itself
and save you lots of frustration, cf. the old "tortoise and the hare"
fable ...

HTH and good luck!

-steve


-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact