Estimated colleagues,
It is probably a simple question, but I am new to limma and I don't
find
the answer.
I have a matrix with columns corresponding to different experiments or
samples, and rows corresponding to genes. In a separate vector of
factors I have a label indicating to which class each sample belongs
to
(it could be mutant or WT, for instance). I read that, in order to
load
data with limma, you have to create a design matrix in which a
filename
for each experiment (or sample) is given... but I have all the
experiments in the same matrix, not in separate files. So, my
(simple)
question is: is there a way to go from my matrix to limma?
Thank you very much,
Federico
On Thursday 13 December 2007 09:38:02 Federico Abascal wrote:
> Estimated colleagues,
> I have a matrix with columns corresponding to different experiments
or
> samples, and rows corresponding to genes. In a separate vector of
> factors I have a label indicating to which class each sample belongs
to
> (it could be mutant or WT, for instance). I read that, in order to
load
> data with limma, you have to create a design matrix in which a
filename
> for each experiment (or sample) is given... but I have all the
> experiments in the same matrix, not in separate files. So, my
(simple)
> question is: is there a way to go from my matrix to limma?
lmFit can deal with a matrix of background corrected normalized M
values.
An example is given in the examples.
The difficult part is constructing the design matrix correctly, and
this only
needs the column names.
# Simulate gene expression data for 100 probes and 6 microarrays
# Microarray are in two groups
# First two probes are differentially expressed in second group
# Std deviations vary between genes with prior df=4
sd <- 0.3*sqrt(4/rchisq(100,df=4))
y <- matrix(rnorm(100*6,sd=sd),100,6)
rownames(y) <- paste("Gene",1:100)
y[1:2,4:6] <- y[1:2,4:6] + 2
design <- cbind(Grp1=1,Grp2vs1=c(0,0,0,1,1,1))
options(digit=3)
fit <- lmFit(y,design)
fit <- eBayes(fit)
fit
as.data.frame(fit[1:10,2])
etc...
best wishes,
ido
