I definitely loaded the package and had a look at the help.start docs.
Neverthelss, I wasn't able to work out my problems that I described in
my previous post.
On Mar 18, 1:58 pm, Henrik Bengtsson <henrik.bengts...@gmail.com>
wrote:
> Hi.
>
> On Thu, Mar 18, 2010 at 6:47 PM, dkny169 <daniela...@yahoo.com> wrote:
> > Unfortunately I cannot get to the docs, unless the same docs are
> > stored under help.start()
>
> Please explain what the problem/error is. Note that you have to load
> a package in order to use ?/help() on its methods, e.g.
>
> library("FIRMAGene");
> ?FIRMAGene
>
> If you don't load it, you get something like:
>
> > ?FIRMAGene
>
> No documentation for 'FIRMAGene' in specified packages and libraries:
> you could try '??FIRMAGene'
>
> The help is the same regardless if you access it via ?/help() or
> help.start(). So, yes, you'll find the same information if you do
> help.start() -> Packages -> FIRMAGene -> FIRMAGene
>
> /Henrik
>
>
>
> > I used following parameters:
> >>plm <- RmaPlm(csNU)
> >> plm
> > [1] "RmaPlm: 0x22388540"
> >>cls<-gsub("TisMap_","",gsub("_0(1-3)_v1_WTGene1","",getNames(cs)))
> >>cls
> > [1] "P.L_10" "P.L_11" "P.L_12" "P.L_14" "P.L_15" "P.L_16" "P.L_2"
> > "P.L_3"
> > [9] "P.L_4" "P.L_5" "P.L_6" "P.L_7" "P.L_8" "P.L_9"
>
> > I am not sure what is supposed to be stored in cls and u.
> > I’m a bit confused however, with what the whole “unique cdf set” is
> > for and how plm is working. Can I save the plm data into a txt file?
> > Many thanks for your help.
> > I really appreciate it.
> > Daniela
>
> > On Mar 16, 4:57 pm, Mark Robinson <mrobin...@wehi.edu.au> wrote:
> >> Hi Daniela.
>
> >> You haven't told us what inputs you've used for 'plm' and 'cls' ...
> >> and what is stored in 'u'?
>
> >> Have you read the docs at:
>
> >> ?FIRMAGene
>
> >> Cheers,
> >> Mark
>
> >> On 14-Mar-10, at 10:21 AM, dkny169 wrote:
>
> >> > Hello,
> >> > I have a question regarding FIRMAGene. Executing the FIRMAGene
> >> > command I get the following error:
> >> >> fg<-FIRMAGene(plm, idsToUse=u, cls=cls)
> >> > Gathering/calculating residuals.
> >> > Reading units.
> >> > Error in if (any(units < 1)) stop("Argument 'units' contains non-
> >> > positive indices.") :
> >> > missing value where TRUE/FALSE needed
>
> >> > The commands used right before are:
>
> >> >> monetaffx<-read.csv("MoEx-1_0-st-v1.na29.mm9.transcript.csv",
> >> >> sep=",",skip=20, header=TRUE,comment.char="",stringsAsFactors=FALSE)
> >> >> probetab<-read.table("MoEx-1_0-st-v1.na29.mm9.probeset.csv",
> >> >> sep="\t", header=TRUE, comment.char="", stringsAsFactors=FALSE)
> >> >> u<-which(getUnitNames(cdf) %in% monetaffx$probeset_id [monetaffx
> >> >> $category =="main" & monetaffx$total_probes >7 & monetaffx
> >> >> $total_probes <200])
>
> >> > I'm not sure what these commands do and how they need to be
> >> > changed to accommodate my own data:
>
> >> > cls <- gsub("TisMap_","",gsub("_0[1-3]_v1_WTGene1","",getNames(cs)))
>
> >> > Many thanks,
> >> > Daniela
>
> >> > --
> >> > When reporting problems on aroma.affymetrix, make sure 1) to run the
> >> > latest version of the package, 2) to report the output of
> >> > sessionInfo() and traceback(), and 3) to post a complete code example.
>
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>
> >> ------------------------------
> >> Mark Robinson, PhD (Melb)
> >> Epigenetics Laboratory, Garvan
> >> Bioinformatics Division, WEHI
> >> e: m.robin...@garvan.org.au
> >> e: mrobin...@wehi.edu.au
> >> p: +61 (0)3 9345 2628
> >> f: +61 (0)3 9347 0852
> >> ------------------------------
>
> >> ______________________________________________________________________
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> >> addressee.
> >> You must not disclose, forward, print or use it without the permission of
> >> the sender.
> >> ______________________________________________________________________
>
> > --
> > When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> > version of the package, 2) to report the output of sessionInfo() and
> > traceback(), and 3) to post a complete code example.
>
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--
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