[BioC] simpleaffy

Rudy.vanEijsden at GEN.unimaas.nl Rudy.vanEijsden at GEN.unimaas.nl
Tue Apr 6 11:39:13 CEST 2004

Hi Simon,

I use simpleaffy in R1.8.1, so I can only tell you what I did to load in my
data. Maybe in the meanwhile somethings have changed.

You need to make a tab delimited text file containing your filenames in the
first column and your sample-code in the second column and name it for
instance "covdesc".
See the short example below:

pat1.cel	P
pat2.cel	P
pat3.cel	P
cont1.cel	C
cont2.cel	C

If you read in your data using the read.affy command, the program knows
which samples are "patient" samples and which samples are "control" samples.
Then you should used the following to read in your data (*.cel files and the
covdesc-file need to be in your working directory):

>raw.data <- read.affy(covdesc="covdesc")



-----Original Message-----
From: Simon Kidd [mailto:kidd at mail.rockefeller.edu]
Sent: Saturday, April 03, 2004 12:12 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] simpleaffy


Iam trying to run simpleaffy.  Iam running R1.9 beta with Raqua and I 
have installed the simpleaffy library, after I load the library I 
follow the vignette:

>  raw.data <- read.affy()

and get the following error message:

Error in file(file, "r") : unable to open connection
In addition: 
Warning message: 
cannot open file `covdesc'

Does anyone know what this means?



Bioconductor mailing list
Bioconductor at stat.math.ethz.ch

More information about the Bioconductor mailing list