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[Bio-software] R-package: How to load a matrix from file to Limma for ebays ??

polen.t2006 from freenet.de via bio-soft%40net.bio.net (by polen.t2006 from freenet.de)
Mon Jul 16 09:08:02 EST 2007

Hi all,

I need a little help in R for determination of differentially
expressed genes using limma.

Example: I have a simple tab-delimeted text-file containg normalized
red/green-Ratio-values of three independent repetitions. In this file
first row contains the names of the experiments and first columns the
names of the probes. Sometimes  there are missing values.

I tried to load the text-file into an object to handle it with limma
for some statistics to determine differentially expressed genes.
However, somehow there is a problem to bring the matrix from the file
to the right limma-object:

1.) data <- read.delim("R_test_matrix.dat ", header = TRUE, sep ="\t",
quote="\"", dec=".", fill = TRUE)

2.) fit <- lmFit(data, design=c(1,1,1))
Error: (subscript) boolean Index to long

3.) fit <- eBayes(fit)
4.) write.fit(fit, file="fit.txt")

Actually, there is no problem when starting from the 3 gpr-files using
another R-script. But in special cases there are pre-processed data
of which the ratio values are already in the text-file mentioned above
for further statistics.

Any Idea?
Thanks a lot for help!


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