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 13:18:56 +0100
Subject: Re: [BioC] [marray] Importing SMD files into marray
To: "michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk>


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