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
Hello,
you can try to post your question to group4bioinformatics :
http://groups-beta.google.com/group/group4bioinformatics?hl=en
There are expert of this field in this group.
Fred
