Entering edit mode
I randomly sucked in a bunch of old HumanMethylation27k files into the
shiny
new beadarray package (which is great, by the way) and saw:
> summary(nObservations(bsd)[,1] - nObservations(bsd)[,13])
Min. 1st Qu. Median Mean 3rd Qu. Max.
-6.000000 0.000000 0.000000 -0.004919 0.000000 8.000000
> colnames(nObservations(bsd))[c(1,13)]
[1] "Grn:5543338058_A" "Red:5543338058_A"
That seems odd -- aren't there supposed to be the same number of beads
in
the red channel as the green (they're all just scanned twice, rite)?
I figured I'd read in a bunch of 27k chips before going to town on the
450k
chips, which currently only give me .idat files to crack open. The
other
irritating little niggles should provide endless entertainment, but
the
newer chips seem to at least have vastly superior control probes.
Great, great, great revision to the data structures and overall
package.
It's really quite usable now for methylation arrays.
Almost forgot:
> sessionInfo()
R version 2.13.0 Under development (unstable) (2010-10-15 r53334)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] methylumiCSV_1.12 matrixStats_0.2.2 R.methodsS3_1.2.1
methylumi_1.5.0
[5] beadarray_2.1.1 Biobase_2.11.2 plyr_1.2.1 reshape2_1.0
loaded via a namespace (and not attached):
[1] grid_2.13.0 lattice_0.19-13 limma_3.7.8 stringr_0.4
[5] tools_2.13.0
--
If people do not believe that mathematics is simple, it is only
because they
do not realize how complicated life is.
John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html="">
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