selSpots: Select spots to use in normalisation

In maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis

Description

Function to select spots to be used in microarray normalisation.

Usage

selSpots(obj=NULL, sigNoise=1, rmFlag=NULL, gLabelsID=c("Name"),
         remove=list(c("BLANK","DAP","LYS","PHE","Q_GENE","THR","TRP")),
         badSpots=NULL, badLabel=NULL)

Arguments

obj	object of class maigesRaw.
sigNoise	positive real number indicating the cutoff to remove spots with signal-to-noise ratio below it.
rmFlag	vector of flag symbols to be removed (for normalisation). These flags are stored in the slot Flags from maigesRaw class.
gLabelsID	character vector indicating the gene labels to be searched to exclude that ones specified in remove argument.
remove	list of same length as GlabelsID containing character vector indicating the symbols of spots to be removed, according to the GlabelsID argument.
badSpots	index of bad spots (numeric or logical) identifying bad spots. May be the gene labels, with label ID specified by the argument badLabel.
badLabel	character string specifying the gene label ID for remove badSpots.

Details

This function takes the object of class maigesRaw and actualise the slot UseSpots according with the arguments passed to the function. This slot is read by the normalisation functions normLoc, normOLIN, normRepLoess, normScaleLimma and normScaleMarray to use only the spots that passed the criteria specified here.

Value

This function returns another object of class maigesRaw with the UseSpots slot actualised.

Author(s)

Gustavo H. Esteves <[e-mail]>

Examples

## Loading the dataset
data(gastro)

## Filtering all spots with signal2noise ratio (Sf/Sb or Rf/Rb) greater
## or equal to 1 and that have 'Name' label as 'BLANK', 'DAP', ..., 'TRP'.
gastro.raw2 = selSpots(gastro.raw, sigNoise=1, rmFlag=NULL, gLabelsID="Name",
  remove=list(c("BLANK","DAP","LYS","PHE","Q_GENE","THR","TRP")))

## To see the number of spots that suvived the filtering above do
apply(gastro.raw2@UseSpots, 2, sum)

## To do the same filtering as above, also filtering flags marcke as 1
## and 4 do
gastro.raw2 = selSpots(gastro.raw, sigNoise=1, rmFlag=c(1,4), gLabelsID="Name",
  remove=list(c("BLANK","DAP","LYS","PHE","Q_GENE","THR","TRP")))

apply(gastro.raw2@UseSpots, 2, sum)

maigesPack documentation built on Nov. 8, 2020, 6:23 p.m.