prepareMaskedAffybatch {maskBAD} | R Documentation

## 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.

### 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.

### Value

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

### Author(s)

Michael Lachmann, Mehmet Somel, Michael Dannemann, Anna Lorenc

### 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

[Package maskBAD version 1.32.0 Index]