maskBAD (version 1.12.0)

prepareMaskedAffybatch: Creating a new CDF

Description

Create a new affyBatch, withprobes and probesetsdefined by mask.

Usage

prepareMaskedAffybatch(affy,cdfTablePath,exmask="none",cdfName="new_cdf",exclude=NA,cutoff=0.2)

Arguments

affy

An object of class AffyBatch.

cdfTablePath

Location of the probe information table. This is a plain text file with probes to build new cdf. It should contain 3 or 5 columns. Column 1: Probeset ID. Column 2: probe x-coordinate. Column 3: probes y-coordinate. Optional column 4: Mismatch probe x-coordinate. Optional column 5: Mismatch probe y coordinate.

exmask

Data frame with probe information, for example first element of the output of function mask. Should contain: column 1: probe x-coordinate, column 2:probe y coordinate, column 3 :probeset, column 4: quality score: values to based filtering on, probes with values smaller than cutoff are discarded.

cdfName

Name for the new CDF.

cutoff

With mask.object, defines the minimum quality score necessary for a probe to qualify to the new cdf.

exclude

Default 'NA'. If exclude set to a number>0, probesets with less than 'exclude' probes remaining after masking are excluded from the new affyBatch object.

Value

newAffyBatch

A list with an affyBatch object and an environment for the new CDF identifier.

Details

The function prepareMaskedAffybatch creates a new affyBatch including only the probes remaining after masking. Set of probes might be defined by a txt file, with cdfTablePath argument, or by a data frame mask.object and cutoff the probes have to exceed to be used in the new cdf.

References

Dannemann et al, The effects of probe binding affinity differences on gene expression measurements and how to deal with them. Bioinformatics 2009

See Also

mask, overlapExprExtMasks, plotProbe

Examples

## prepare new affy batch after masking
## using the expression mask object from the example of the mask function
data(AffyBatch)
data(exmask)
## AffyBatch object before masking
newAffyBatch
affyBatchAfterMasking <-
   prepareMaskedAffybatch(affy=newAffyBatch,exmask=exmask$probes)
## AffyBatch object after masking
affyBatchAfterMasking