[BioC] DEXSeq: Creating Sample

[Martin Morgan]

On 05/25/2013 05:55 PM, Margaret Linan wrote:
> Hi-
>
> I tried to apply my files to the samples code given by the pasilla vignette
> and got an error. Note, the count.txt file has only two columns. Currently,
> I lack the information ( don't know how get it ), to accurately specify the
> condition=   portion of the code below.
>
> samples=data.frame(condition=c(rep("treated", 3), rep("untreated",4)),
> row.names=(file.path("/home/mlinan", mustWork=TRUE), pattern="count.txt"),
> stringsAsFactors=TRUE, check.names=FALSE)
>
> Error: unexpected ',' in "samples=data.frame(condition=c(rep("treated", 3),
> rep("untreated",4)), row.names=(file.path("/home/mlinan", mustWork=TRUE),"

The error says that there is a ',' in a location in the command that you've 
entered where one was not expected. Usually this is because of mis-placed 
parentheses, but in this case you've written

   row.names=(file.path("/home/mlinan", mustWork=TRUE), pattern="count.txt"),

but maybe meant to write

   row.names=file.path("/home/mlinan", pattern="count.txt", mustWork=TRUE),

R allows one to write very dense code like this, but a useful strategy is to 
develop complicated expressions by composing them from simpler lines that you 
know work, e.g., verifying that file.path("/home/mlinan", pattern="count.txt", 
mustWork=TRUE) returns something sensible, before trying the more complicated 
instruction. (A common typo for me is to mis-spell 'mustWork=TRUE'; R then 
returns a file path that doesn't work, because it doesn't recognize the 
mis-spelled argument and tries to use 'TRUE' as part of the path). Be sure to 
consult the help pages

   ?file.path

for details on how functions are to be used; the help pages may be intimidating 
at first, but they end up being helpful.

It can be helpful to work from the R script files that most (though not all) 
vignettes use. These are available from the package 'landing page'; I'm not sure 
where the code chunk above is supposed to come from, but the DEXSeq landing page 
is at

   http://bioconductor.org/packages/release/bioc/html/DEXSeq.html

and the code used to generate the vignette is linked to that page, at

   http://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.R

Actually, the vignette and script are installed with the package; the vignette 
is accessible with

   vignette(package="DEXSeq")       ## discover available vignettes
   vignette("DEXSeq")               ## open the vignette

and the code in the vignette can be evaluated, in your own session, with

   pdf = vignette("DEXSeq")$pdf      ## path to vignette
   script = sub(".pdf", ".R", pdf)  ## path to script
   source(script, echo=TRUE, max=Inf)  ## evaluate all the code

Sometimes packages 'suggest' other packages that are used in the vignette, and 
it is necessary to install those to evaluate the vignette code successfully.

Martin


>
> Any help is appreciated.
>
> Thanks,
> ML
> ASU Grad Student
>
> 	[[alternative HTML version deleted]]
>
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