call.exprs {simpleaffy}R Documentation

Generate Expression Summaries for Affymetrix Data

Description

Generates expression summaries and normalizes Affymetrix data using either MAS5.0, GCRMA or RMA algorithms.

Usage

call.exprs(x, algorithm = "rma", do.log = TRUE, sc = 100, method = NA)

Arguments

x

an AffyBatch object

algorithm

one of '"rma","rma-R","gcrma", "mas5", "mas5-R". "rma" and "mas5" make use of a native C-library and are faster than "rma-R" and "mas5-R".

do.log

return logged data if true

sc

if the mas5 algorithm is being used, sets the target intensity to which the chips should be scaled.

method

The algorithm used to normalise the data. Has no effect for "rma", defaults to quantile normalisation for "rma" and no normalisation for "mas5"

Value

An AffyBatch object containing expression summaries.

Author(s)

Crispin J Miller

References

http://bioinformatics.picr.man.ac.uk/

See Also

read.affy, expresso, justRMA, justMAS

Examples

 
  ## Not run: 
    eset.rma  <- call.exprs(eset,"rma"); 
    eset.mas5 <- call.exprs(eset,"mas5"); 
  
## End(Not run)
[Package simpleaffy version 2.54.0 Index]