addManifest |
Add annotation data |
annotation,beadQC-method |
Class "beadQC" |
annotation<-,beadQC,ANY-method |
Class "beadQC" |
annotation<-,beadQC-method |
Class "beadQC" |
batchAnalysis |
Batch Analysis |
beadAnalysis |
Automated Bead Analysis |
beadData-class |
Class "beadData" |
beadQC-class |
Class "beadQC" |
boxplot,beadData-method |
Class "beadData" |
boxplotArrays |
Plot a series of QC boxplots |
boxplotQC |
Plot a subset of QC boxplots |
clusterplot |
Plots a hierarchical cluster plot |
cutoff |
Determine the number of transcripts that pass a fold change cut-off criteria |
detectionCalls |
Get percentage of genes called present |
detectionCalls,beadData-method |
Class "beadData" |
detExprs |
Accessor Methods for beadData class |
detExprs,beadData-method |
Class "beadData" |
dotplotArrays |
Plots a series of dotplots for BeadChip QC data |
dotplotQC |
Plot a subset of QC dotplots |
examplebeadData |
An example of a beadData object |
examplebeadQC |
An example of a beadQC object |
extract |
Extract columns from a BeadStudio file |
fileOrigin |
Accessor Methods for beadData class |
fileOrigin,beadData-method |
Class "beadData" |
fileOrigin,beadQC-method |
Class "beadQC" |
filterData |
Filter data based on detection score |
getAnnot |
Get annotation information |
getArrayStats |
Get QC values for a BeadChip |
getDet |
Get detection scores for a given gene(s) |
getExprs |
Get expression intensities for a given gene(s) |
getID |
Get expression data for a given gene ID |
getQC |
Generate QC data |
getQC2 |
Generate QC data |
htmloutput |
Produce an html summary report |
HumRef8 |
A mapping file of Illumina Probe IDs to control type |
HumWG6 |
A mapping file of Illumina Probe IDs to control type |
multiDensity |
Plot multiple density functions |
multiecdf |
Plot multiple estimated cumulative density function graphs |
nGenes |
Accessor Methods for beadData class |
nGenes,beadData-method |
Class "beadData" |
normalise |
Normalise a beadData object |
normMethod |
Accessor Methods for beadData class |
normMethod,beadData-method |
Class "beadData" |
nSamples |
Accessor Methods for beadData class |
nSamples,beadData-method |
Class "beadData" |
pairs,beadData-method |
Class "beadData" |
param |
Accessor Methods for beadData class |
param,beadData-method |
Class "beadData" |
pc |
Principal component plot |
plot,beadData,missing-method |
Class "beadData" |
plotSamples |
QC sample plots |
readBead |
Read BeadStudio expression data file |
readManifest |
Read annotation data |
readQC |
Reads log file data |
sampleQC |
Accessor Methods for beadData class |
sampleQC,beadQC-method |
Class "beadQC" |
scatterPlot |
Pairwise scattergraph of data |
signalMeans |
Accessor Methods for beadData class |
signalMeans,beadData-method |
Class "beadData" |
summary,beadData-method |
Class "beadData" |
write.beadData |
Write beadData to a file |
writeQC |
Writes QC data to a log file |
[,beadData-method |
Class "beadData" |
[,beadQC-method |
Class "beadQC" |