(cc:'ing the epigenomicsforum list due to a similar request there)

You can now coerce (at least in devel) without the OOB probes (I checked in
an additional fix Monday morning, which was also needed to correct a build
issue), but you will still run into issues with minfi's approach.  There
are at least two possibilities to get around this and still get estimated
cell counts.  Note that I'd choose #2 (or a reasonable semblance of it,
i.e. quantile normalizing your data together with Reinius & Kere's sorted
leukocyte fractions) whenever feasible, but sometimes it isn't feasible.
Here's one way to deal with a lack of raw binary files (#1), and some notes
about Jaffe's approach (#2).

1) Use the modified version of the modified version of Houseman's code
(yes, that's in there twice!)

require(devtools)
install_github('chromophobe','ttriche')

?composition  ## I don't write man pages just for fun...
require(FlowSorted.Blood.450k)
counts <- getBloodCellCounts(your.GenomicRatioSet.coerced.from.lumi)
plotCellCounts(counts)


2) Start from the IDATs, if you have them, in which case you can just run
the whole thing in minfi.  Sometimes this is impossible (original authors
blithely ignore you, otherwise-extremely-helpful program officer for their
grant gets buried by a snowstorm, etc.) so I yanked out the essential bits
and stuffed them into a convenience function above.  One of these days I'll
tidy up chromophobe enough to push it into BioC.  But, if you have raw data
(and technical or biological replicates), it would be worth comparing the
two approaches to see whether your additional processing steps are helping
enough to keep them around.  I may end up doing so (and perhaps comparing
both with EWASher).


Hope this helps,

--t


On Sat, Feb 8, 2014 at 10:15 AM, Aileen Bahl <aileen.bahl@helsinki.fi>wrote:

> Dear all,
>
> I used lumi to analyze my 450k data. Now, I want to use the Houseman
> algorithm to correct for the cell composition. As far as I read, the
> implementation in minfi covers several changes of the algorithm for the
> 450k platform. Therefore, I would like to use this package instead of
> changing the original code by hand. However, while trying to use minfi, I
> faced the problem of transforming my MethylumiM object to the required
> RGChannel object. I already found the coercions.R from Bioconductor but
> this gives me an error because the full OOB intensities are missing. Could
> you please provide some help on how to make this transformation in both
> directions (MethylumiM to RGchannel and the other way around)?
>
> Thanks in advance,
> Aileen
>
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