mask {maskBAD} | R Documentation

## Filtering/Masking expression data

### Description

Identyfying probes with binding affinity difference (BAD probes) between two groups of samples on the basis of expression data.

### Usage

    mask(affy,exprlist=NULL,useExpr=TRUE,ind,PM=FALSE,verbose=TRUE)

### Arguments

`affy` | An object of class `AffyBatch`.
`exprlist` | A vector with probesetnames to be used. If NULL, all probesets are analyzed.
`useExpr` | Logical. If 'TRUE', only expressed genes (see Details) are used. If 'FALSE', all probes are analyzed.
`ind` | Numeric vector, with values 1 and 2, definining group assignement for samples in `affy`.
`PM` | Logical. If 'TRUE', only probes with a mean pm value greater than the mean mm value are used.
`verbose` | Logical. If 'TRUE', it writes out some messages indicating progress. If 'FALSE' nothing should be printed.

### Details

The function `mask` identifies in expression data probes which binding affinity (BAD probes) differs between two groups of samples, e.g two species. The basic input data is `AffyBatch object`(expresssion data prepared using the function `ReadAffy` from the library `Affy`) and a vector defining group assignement of samples. As masking is based on expression values, only expressed probes should be used. As a default they are defined by the `affy` function `mas5calls` and condition of being expressed (having "P" value) in at least 90% of samples from each group, but any set of probesets might be submitted with `exprlist` argument. Probes are analyzed for difference in binding affinity between groups. Each probe is assigned a quality score, based on all pairwise probes' correlations within probesets (for details see vignette or paper). Probes' quality scores, their x and y coordinates on the microarray and the probeset names are stored in a matrix.

### Value

A list of two objects will be returned.

`probes` | A data frame with x,y coordinates, quality score and probeset for each analyzed probe.
`notUsed` | If PM=TRUE: A vector with unused probes having a lower pm mean value than mm mean value.

### Author(s)

Michael Dannemann, Michael Lachmann

### References

Dannemann et al, The effects of probe binding affinity differences on gene expression measurements and how to deal with them. Bioinformatics 2009 \ Khaitovich et al,Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees, Science 2005

### See Also

`overlapExprExtMasks, prepareMaskedAffybatch, mas5calls, plotProbe`

### Examples

    data(AffyBatch)
    ## we provide 20 samples (10 for both human and chimpanzee)
    ## the first 10 entries are chimpanzee samples the last 10 from human
    ind.vec=rep(1:2,each=10)
    ## mask on AffyBatch with all genes
    exmask <-
    mask(newAffyBatch,ind=ind.vec,PM=TRUE,useExpr=FALSE)

[Package maskBAD version 1.36.0 Index]