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

J.Oosting at lumc.nl J.Oosting at lumc.nl
Wed Oct 1 16:16:43 CEST 2008

You should take a look at the limma analysis of affymetrix and other
single-channel designs, as this is what you have now basically.
The examples in the userguide on this type of data do not need a
targets.txt file.

> I have a question about reading in data for use with the Limma package
> 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
> will be used for educational purposses only. I've been working on a
> 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
> which I hope to finish on friday, so any help to point in the right
> direction is greatly appreciated.

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