[BioC] [marray] Importing SMD files into marray

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Thu Mar 17 12:26:35 CET 2005

Hi Rene

What does:


Produce?  Is 28380.xls in your current working directory?


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Rene
Sent: 17 March 2005 11:15
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] [marray] Importing SMD files into marray


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

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