Package: gcrma 2.85.0

Z. Wu

gcrma: Background Adjustment Using Sequence Information

Background adjustment using sequence information

Authors:Jean Wu, Rafael Irizarry with contributions from James MacDonald <[email protected]> Jeff Gentry

gcrma_2.85.0.tar.gz
gcrma_2.85.0.zip(r-4.7)gcrma_2.85.0.zip(r-4.6)gcrma_2.85.0.zip(r-4.5)
gcrma_2.85.0.tgz(r-4.6-x86_64)gcrma_2.85.0.tgz(r-4.6-arm64)gcrma_2.85.0.tgz(r-4.5-x86_64)gcrma_2.85.0.tgz(r-4.5-arm64)
gcrma_2.85.0.tar.gz(r-4.7-arm64)gcrma_2.85.0.tar.gz(r-4.7-x86_64)gcrma_2.85.0.tar.gz(r-4.6-arm64)gcrma_2.85.0.tar.gz(r-4.6-x86_64)
gcrma_2.85.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
gcrma/json (API)
NEWS

# Install 'gcrma' in R:
install.packages('gcrma', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On BioConductor:gcrma-2.85.0(bioc 3.24)gcrma-2.84.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarrayonechannelpreprocessing

7.39 score 11 packages 182 scripts 2.1k downloads 186 mentions 31 exports 13 dependencies

Last updated from:b5a7b90c54. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR171
linux-devel-arm64NOTE195
linux-devel-x86_64NOTE225
source / vignettesOK210
linux-release-arm64NOTE193
linux-release-x86_64NOTE229
macos-release-arm64NOTE191
macos-release-x86_64NOTE279
macos-oldrel-arm64NOTE170
macos-oldrel-x86_64NOTE461
windows-develNOTE436
windows-releaseNOTE450
windows-oldrelNOTE433
wasm-releaseOK127

Exports:average.for.PAVbase.profilesbase.profiles.mmbase.profiles.ncbg.adjust.affinitiesbg.adjust.constantbg.adjust.fullmodelbg.adjust.gcrmabg.adjust.mmbg.adjust.opticalbg.parameters.nscheck.probescompute.affinitiescompute.affinities.localcompute.affinities2compute.affinity.coeffast.bkggcrmagcrma.bg.transformationgcrma.bg.transformation.fastgcrma.enginegcrma.engine2getCDFgetProbePackageGSB.adjjust.gcrmajustGCRMAleft.sigmamem.bkgPAVplotBaseProfiles

Dependencies:affyaffyioBiobaseBiocGenericsBiocManagerBiostringscrayongenericsIRangespreprocessCoreS4VectorsSeqinfoXVector

gcrma1.2

Rendered fromgcrma2.0.Rnwusingutils::Sweaveon May 30 2026.

Last update: 2013-11-01
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Spline coefficients for estimation of affinity from probe sequenceaffinity.spline.coefs
Background adjustment with sequence information (internal function)bg.adjust.affinities bg.adjust.constant bg.adjust.fullmodel bg.adjust.mm bg.adjust.optical
GCRMA background adjust (internal function)bg.adjust.gcrma
Estimation of non-specific Binding Background Parametersaverage.for.PAV bg.parameters.ns left.sigma PAV
Probe Affinity computationbase.profiles base.profiles.mm base.profiles.nc check.probes compute.affinities compute.affinities.local compute.affinities2 compute.affinity.coef plotBaseProfiles
Robust Multi-Array expression measure using sequence informationgcrma gcrma.bg.transformation gcrma.bg.transformation.fast GSB.adj
GCRMA background adjust engine(internal function)gcrma.engine
GCRMA background adjust engine(internal function)gcrma.engine2
Compute GCRMA Directly from CEL Filesjust.gcrma justGCRMA