methylumi 2.20.0
Sean Davis
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/methylumi | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | [ OK ] | OK | WARNINGS | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL methylumi
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
* installing *source* package ‘methylumi’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
3 HumanMethylation27 samples found
0 HumanMethylation450 samples found
Attempting to extract protocolData() from list...
Determining chip type from IDAT protocolData...
Note: method with signature ‘methylData#character’ chosen for function ‘sampleNames<-’,
target signature ‘MethyLumiQC#character’.
"eSet#ANY" would also be valid
Background mean & SD estimated from 24156 probes
Loading required package: MASS
Attaching package: ‘MASS’
The following object is masked from ‘package:AnnotationDbi’:
select
Background mean & SD estimated from 31000 probes
HumanMethylation27 data encountered, skipping...
Object Information:
MethyLumiSet (storageMode: lockedEnvironment)
assayData: 27578 features, 3 samples
element names: betas, methylated, methylated.OOB, pvals, unmethylated, unmethylated.OOB
protocolData: none
phenoData
sampleNames: 5318317007_A 5318317007_B 5318317007_C
varLabels: barcode mu.Cy3 ... offset.Cy5 (9 total)
varMetadata: labelDescription
featureData
featureNames: cg00000292 cg00002426 ... cg27665659 (27578 total)
fvarLabels: Probe_ID DESIGN COLOR_CHANNEL
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: IlluminaHumanMethylation27k
Major Operation History:
submitted finished
1 2017-04-14 15:34:20 2017-04-14 15:34:21
2 2017-04-14 15:34:21 2017-04-14 15:34:21
3 2017-04-14 15:34:21 15:34:22
command
1 methylumIDAT(barcodes = getBarcodes())
2 Subset of 27578 features.
3 methylumi.bgcorr(x = methylumIDAT(getBarcodes()))
** installing vignettes
‘methylumi.Rnw’
‘methylumi450k.Rnw’
** testing if installed package can be loaded
* DONE (methylumi)