simpleaffy (version 2.48.0)

get.annotation: Get annotation data for a gene list

Description

Takes a vector of probeset names and a CDF name. Produces a table of annotations, containing gene name, description, sequence accession number and unigene accession number for each probeset. In addition, write.annotation is a utility function that outputs the annotation data in a form suitable for loading into excel and results.summary takes the outut of pairwise.comparison or pairwise.filter and spits out a table with the means of the replicates the fold-change between them (log2) and t-test p-values. This is followed by a table of annotation (produced by get.annotation).

Usage

get.annotation(x, cdfname,verbose=FALSE)
write.annotation(summary,file="results/annotation.table.xls")
results.summary(results,cdfname)

Arguments

x

a vector of probe names

cdfname

the name of the chip (as produced by cdfName(AffyBatch)

verbose

print out information if problems are found looking things up in the annotation data

summary

a table of data to write in a format appropriate to read into Excel

file

a table delimited file

results

a PairComp object, as produced by pairwise.comparison and pairwise.filter

Value

A table containing annotation data

References

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

Examples

 ## Not run: 
#    pw       <- pairwise.comparison(eset.rma,"group",c("A","P"))
#    pw.filtered <- pairwise.filter(pw)
#    summary     <- results.summary(pw.filtered,"hgu133a")
#    write.annotation(file="spreadsheet.xls",summary)
#   ## End(Not run)