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

Fred via bio-soft%40net.bio.net (by frederic.fleche from gmail.com)
Thu Aug 16 02:37:48 EST 2007

On Jul 16, 4:08 pm, polen.t2... from freenet.de wrote:
> 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!
> Ciao,
> TP


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