[BioC] Need help using read.table to read in non-standard data

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Wed Oct 1 10:53:10 CEST 2008

What are the actual data?  Raw intensities or log2 ratios?

You can either create an RGList object (if the data are raw intensities)
or an MAList object (if they are log ratios).  You could also create log
ratios from the data and then create an MAList object.

The problems comes if you only have data for one channel (red or
green?!) or you only have log ratios (where would you get A from?

We need more information


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of
m_kempenaar at planet.nl
Sent: 01 October 2008 09:17
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Need help using read.table to read in non-standard data


I have a question about reading in data for use with the Limma package
by using standard R functions like read.table as mentioned in chapter
The data I'm trying to use is an existing dataset from the DeRisi lab
and will be used for educational purposses only. I've been working on a
script to preprocess/ normalize the data using standard R functions
after which I have a data frame containing the following columns (9
columns and 5969 rows):

ORF (Identifier)
Name (Gene name (optional))
T1 - T7 (normalized log intensities for each of the 7 arrays)

Other then the above I have no information about the data so I cannot
create a targets.txt file etc. Is there any way that I can use Limma to
do the normalization and analysis on this data?

I'm trying to write a short tutorial on how to use Limma with this data
which I hope to finish on friday, so any help to point in the right
direction is greatly appreciated.

M. Kempenaar
Hanze University
Groningen, the Netherlands

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