| get.annotation {simpleaffy} | R Documentation |
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).
get.annotation(x, cdfname,verbose=FALSE) write.annotation(summary,file="results/annotation.table.xls") results.summary(results,cdfname)
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 |
A table containing annotation data
Crispin J Miller
http://bioinformatics.picr.man.ac.uk/
## 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)