Hi all,

Our lab analyzes gene-expression from microarray and RNAseq platforms.
Currently, I am looking for a package to test differential expression (DE)
while considering continuous variables that may alter gene-expression
profiles. In other words, an ANCOVA type tool. I am quite familiar with
Limma (ANOVA) but including continuous variables is not very well described.

Specifically, we have a project were two groups can be modeled over the
same 2 time points. One group starts healthy and ends in a disease state.
The other group starts healthy and remains healthy.

We are interested in identifying genes uniquely responding within one group
and not in the other. Thus, we have implemented a longitudinal contrast
with linear modeling through Limma. However, we are also interested in
adding one or two continuous variables (tumor size, time spent meditating,
the amount of drinks one consumes etc..)  to check if gene expression
differences or similarities may be due to these factors instead of due to
belonging to a certain class. Limma seems to test categorical variables,
but I don't think it is capable of either correlating gene-expression to
continuous variables.

If not, can someone recommend  a tool which may be appropriate for such a
situation?

Yours,

Michael

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