Hi all,

I have time course gene-expression from blood at 4 different time points.
During the last two time points we see an increase in various different
cell-type frequencies. We are interested in correcting our gene expression
matrix with numerous continuous variables, that is estimated cell-type
frequency. However, I realize that Combat does not correct for continuous
batches, but rather continuous variables.

In this scenario, I have no batch effects however I am interested in using
the continuous variables (cell-type frequencies) to correct our gene
expression matrix.

1. What does the function "numCovs" implement exactly and how does it
handle continuous variables? What is the result on the gene-expression
matrix?

2. If correcting the matrix is not feasible, we may consider simply using
cell-type frequencies as continuous variables in an ANCOVA.

Yours,

Michael

-- 
M.S. Breen
PhD, Bioinformatics and Genomics
Clinical and Experimental Sciences
Univ. of Southampton

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