Fwd: [BioC] [marray] Importing SMD files into marray

[Rene Nederhand]

---------- Forwarded message ----------
From: Rene Nederhand <r.nederhand at gmail.com>
Date: Thu, 17 Mar 2005 13:28:33 +0100
Subject: Re: [BioC] [marray] Importing SMD files into marray
To: "michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk>


Nick,

Your message did point me in the good direction. I tried again, but
now starting R in the working directory and this works fine.

> files=c("28370.xls")
> read.SMD(fnames=files, path=datdir, DEBUG=TRUE)
[1] "28370.xls"
Generating layout from 28370.xls
Error in read.SMD(fnames = files, path = datdir, DEBUG = TRUE) :
        Object "datdir" not found
> read.SMD(fnames=files, path=datadir, DEBUG=TRUE)
[1] "28370.xls"
Generating layout from 28370.xls
[1] "Reading Gal file"
[1] "done \n "
Generating target sample info from all files
[1] "Ch1 Intensity \\(Median\\)"
[1] "comment = 21"
Calling read.marrayRaw ...
Reading ...  ~/Desktop/28370.xls
An object of class "marrayRaw"
@maRf
[1] 5484 4263 8637 8722 4975
43003 more rows ...
.....

Thanks for your help!

Kind regards,

Rene


On Thu, 17 Mar 2005 13:18:56 +0100, Rene Nederhand
<r.nederhand at gmail.com> wrote:
> Hi Nick,
>
> Thanks for your reaction.
>
> readLines("28370.xls") gives the following output:
>
> > readLines("28370.xls")
> Error in file(con, "r") : unable to open connection
>
> Since I started R from "/Applications/R" (I'm using a Mac) and the
> file is on "~/Desktop" this is what I would assume. Using the full
> path works fine:
>
> > readLines("~/Desktop/28370.xls")
>     [1] "!Exptid=28370"
>     [2] "!Experiment Name=hyperinsulinemic clamp in human muscle"
>     [3] "!Organism=Homo sapiens"
> .....lots of lines....
>
> For your information: I am using R V2.01, latest Bioconductor (updated
> yesterday) and marray V1.5.25 (latest development packages; stable
> package gives the same problem).
>
> Any idea?
>
> Kind regards,
> Rene
>
>
> On Thu, 17 Mar 2005 11:26:35 -0000, michael watson (IAH-C)
> <michael.watson at bbsrc.ac.uk> wrote:
> > Hi Rene
> >
> > What does:
> >
> > readLines("28370.xls")
> >
> > Produce?  Is 28380.xls in your current working directory?
> >
> > Mick
> >
> > -----Original Message-----
> > From: bioconductor-bounces at stat.math.ethz.ch
> > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Rene
> > Nederhand
> > Sent: 17 March 2005 11:15
> > To: bioconductor at stat.math.ethz.ch
> > Subject: [BioC] [marray] Importing SMD files into marray
> >
> > Hi,
> >
> > This is probably a newbie question, but I've been looking for a solution
> > for ours.
> >
> > I am trying to import a SMD file (exptID=2641) into the marray package.
> > Unfortunately this seems to fail every time:
> >
> > > datadir="~/Desktop"
> > > fnames=c("28370.xls")
> > > read.SMD(fnames=fnames, path=datadir,DEBUG=TRUE)
> > [1] "28370.xls"
> > Generating layout from 28370.xls
> > [1] "Reading Gal file"
> > [1] "done \n "
> > Generating target sample info from all files
> > [1] "Ch1 Intensity \\(Median\\)"
> > Error in file(con, "r") : unable to open connection
> >
> > I have even tried to download the corresponding gal file from Standford,
> > but this doesn't work either.
> >
> > In addition, I tried using the read.SMD2 function that somebody posted
> > here a while ago:
> >
> > > read.SMD2(fnames=fnames, path=datadir,DEBUG=TRUE)
> > [1] "~/Desktop/28370.xls"
> > [1] NA
> > Generating layout from 28370.xls
> > Error in if (skip > 0) readLines(file, skip) :
> >         missing value where TRUE/FALSE needed
> >
> > Help! What should I do to make this thing work? Microarray and
> > Bioconductor are new to me, but this should work, doesn't it?
> >
> > Kind regards,
> >
> > Rene Nederhand
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
>
> --
> Rene Nederhand
>

--
Rene Nederhand


-- 
Rene Nederhand