[BioC] ComBat --- Got it working for some variables but not others?!

[Celine Bourdon]

Hi all
 (especially (maybe) to Evan or Evan-LAB-People.. haha)  ... I am trying to
run ComBat to correct my methylation data for batch (which are 11 Slides)
and other covariates.

But to illustrate the problem i reduced the model to it's simplest and
picked 2 variables, one that works and one that does not.

ComBat WORKs for logBF (Body Fat) variable
model <-model.matrix(~logBF, data=phenoData)
cBat_Mvalues <- ComBat(dat=SWANed.Mvalues, batch=Slide,                mod=
model, numCovs=NULL, par.prior =TRUE)

ComBat does NOT WORK for logVF (Visceral Fat) variable
model <-model.matrix(~logBF, data=phenoData)
cBat_Mvalues <- ComBat(dat=SWANed.Mvalues, batch=Slide,                mod=
model, numCovs=NULL, par.prior =TRUE)

I get the following error:
Found 11 batches
Found 1  categorical covariate(s)
Standardizing Data across genes
Error in solve.default(t(design) %*% design) :
  system is computationally singular: reciprocal condition number =
2.2124e-18

I run the exact same script for both variables, on the exact same Mvalue
dataset.
Both variables are quite similar,... and to me seem similarly distributed
between batches but ... maybe someone has more experience looking at
this... and  will tell me other wise?

I include here a correlation matrix between the 2 variables and Batch...

Is my visceral fat (VF) to be considered more "confounded" with batch then
my Body FAt variable (BF) or my BMI? Please see attached image.

These are 2 example variables, I actually have in total 3 variables that
work, and 4 that don't.

Any other input, ideas, would be very very welcome as i have been on this
issue for a longtime now. I tried to illustrate things as best i could,
any help will be very appreciated,
thanks a lot!
c
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