Hello,

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 4.1.
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
Bioinformatics
Hanze University
Groningen, the Netherlands


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