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Martin Bonke
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40
@martin-bonke-2901
Last seen 10.2 years ago
Hello everyone,
I am looking for some help in setting up an analysis protocol in R for
my
microarray dataset. My knowledge of R is still somewhat rudimentary,
but,
having worked with it for about half a year now I do understand the
basics
and can get most of the packages that I've needed to work. However,
the past
week I've been stumped on a certain analysis that I would like to
perform on
my results.
My dataset consists of microarrays of RNAi experiments that affect the
cell
cycle. Part of the results is a phenotypic analysis, where I have the
percentages of cells in the different stages of the cell cycle. Now I
would
like to link this phenotypic data with the microarray data and find
out
whether the expression of genes is linked with a certain stage of the
cell
cycle. So, currently I have the matrix of all my microarray data,
where the
columns are the experiments, and the rows are the genes, and the
values are
their log-fold differences compared to wild type. I also have vectors
that
contain for each experiment the percentage of cells in a specific
stage of
the cell cycle (a vector for G1, one for G2, etc).
Now I am quite at a loss on how to link these two together, I was
suggested
to use a least squares analysis and I've been trying make lsfit() work
for
my data, but so far without luck. The documentation with these
functions
generally is rather hard to understand for me and finding descriptive
guides
on how to do something like this has been very unsuccessful so far,
probably
because I am not really sure how this would be named.
I hope that someone out here understands what I am trying to do and
perhaps
can give me a hint or two on what I should be looking into.
Many thanks in advance.
Martin
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