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.
Thanks a lot for help!