nomadCheckBias: Check level of bias based on batch effect.
In carlmurie/NOMAD: Normalization of Mass Spectrometry Data

Description Usage Arguments Value Examples

Check level of bias based on batch effect.

1 2	nomadCheckBias(dat, fact, numNAs = dim(dat)[[2]], label = NULL, yMax = NULL, showSampleSize = TRUE)

`dat`	`matrix` Rows are protein, columns are samples (each iTRAQ sample per day. The same format as the "scores" element of the output of assembleProteins with format=bySample. Missing data must be shown as NA.
`fact`	`vector` numeric or character vector of labels identifying batches. Generally a batch is a single MS run of 4 or 8 iTRAQ channels.
`numNAs`	`integer` Number of missing data points allowed. Defaults to number of samples in data
`label`	`string` Text for title of graph
`yMax`	`real` Upper count range for plotting histograms.
`showSampleSize`	`boolean` If TRUE add text box showing number of samples.

None

data(BalfPeptides)

## assemble the protein scores without normalization
scores <- nomadAssembleProteins(BalfPeptides$Abundance, BalfPeptides)
runInd <- rep(1:3, each=8)  ## each integer is a single batch (3 batches total)
nomadCheckBias(scores$scores, fact=runInd)