[BioC] ComBat: 3 adjustment variables & continuous adjustment variables

[Steve Lianoglou]

Hi Magda,

You are using a version of R (2.14) that is horribly out of date, and
as a result your bioconductor packages are frozen to versions that are
quite old.

Please update to the latest version of R (3.0.3) and reinstall your
bioconductor packages using biocLite to ensure that you are running
the the latest version of them.

The package you are version (sva v3.0.2) is now at version 3.8.0.

One question you asked:

> - Row would be better treated as a continuous adjustment variable than a factor. In the version of sva that I am using (3.0.2) I believe that only factor adjustment variables are supported. I have seen mention in a few forums that there might be an update to ComBat to adjust for a numeric batch variable, is one available?

Is readily answered by reading through the vignette for the current
version of the package:

http://bioconductor.org/packages/release/bioc/vignettes/sva/inst/doc/sva.pdf

Specifically in Section 7 (Applying the ComBat function to adjust for
known batches), where it states:

"""
By default, all adjustment variables will be treated as factor
variables by the ComBat function. If you would like to include
continuous adjustment variables, also create a vector containing the
column numbers of the continuous covariates in the model matrix. This
vector must then be input into ComBat via the numCovs option.
"""

HTH,

-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech