This is extremely weird.  As far as I know, both packages are using the
same original code for reading in IDAT files, and as far as I can recall,
we (minfi / illuminaio) have not had a bugfix which would address this.
 But you are looking at Beta's so my immediate thought is that you are
doing something with divide by zero and/or na.omit.  I would be shocked if
there is a difference in the Red/Green channel measurements.

Could we get
(1) the offending IDAT file posted somewhere
(2) full code
(3) sessionInfo()

Best,
Kasper


On Wed, Jul 3, 2013 at 9:32 AM, Pilling, Luke <L.Pilling@exeter.ac.uk>wrote:

> Hello,
>
> I am loading 450k methylation data into R and have noticed a difference in
> the way that "methylumi" and "minfi" load the IDAT files.
>
> Each has a dedicated function for this (methylumIDAT() for methylumi, and
> read.450k.exp() for minfi), each of which creates an object which contains
> the relevant information (MethyLumiSet objects in the first instance,
> RGChannelSet objects in the 2nd).
>
> I am finding that the number of "missing" values reported in an array is
> much higher in the MethyLumiSet object than the RGChannelSet object, when I
> compare the 2 methods on the same IDAT files (this is before any
> exclusions, transformations, etc - raw data after import is different).
>
> To give an example;
>
> I loaded a single array (12 samples) using both methods. I extracted the
> betas, and then used the "na.omit()" command to remove any probes (rows)
> that have missing values. I find that 988 probes are excluded from the
> MethyLumiSet object, but not from the RGChannelSet object (47 probes are
> omitted from both).
>
> I then wanted to look at the raw data for a probe that is excluded from
> MethyLumiSet but not RGChannelSet;
>
>
> ###### First I picked the first probe in this list (excluded from
> MethyLumiSet but not RGChannelSet);
>
> > probes.excluded.methylumiset[! probes.excluded.methylumiset %in%
> probes.excluded.rgchannelset][1]
> [1] "cg00035864"
>
> ###### Then extracted the betas for this probe from both data objects;
>
> > methylumiset.betas[row.names(methylumiset.betas) == "cg00035864"]
> [1]        NA        NA        NA        NA 0.2101861 0.2584211        NA
>        NA        NA        NA 0.1878819        NA
> > rgchannelset.betas [row.names(rgchannelset.betas) == "cg00035864"]
> [1] 0.5665025 0.3771760 0.5247209 0.6393211 0.2101861 0.2584211 0.5242291
> 0.4642263 0.4795640 0.5143571 0.1878819 0.4678663
>
>
> I cannot find any reference on the web or in the documentation for these
> functions as to why they would treat the raw IDAT data import differently -
> any input/insight would be much appreciated.
>
> Many thanks,
> Luke
>
> ------------------
> Mr. Luke C. Pilling
> Associate Research Fellow & PhD Researcher,
> Epidemiology and Public Health Group, Medical School, University of
> Exeter, U.K.
>
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