filter.NonUnifOL {Agi4x44PreProcess} | R Documentation |
An internal function to be used by filter.probes
filter.NonUnifOL(ddFILT, limNonUnifOL, ManuelaGO, targets, annotation.package)
ddFILT |
an RGlist object |
limNonUnifOL |
for a given feature xi accros samples, is the maximum in a experimental condition with a saturation-FLAG = 1 (Is Non Uni OL) |
ManuelaGO |
logical, if a known annotation package is available then
it is TRUE |
targets |
data.frame with the target structure |
annotation.package |
a character specifying the AGI annotation package: 'hgug4112a.db','mgug4122a.db' |
To keep good quality probes, we filtered out probes that has more than y in at least one experimental condition with a flag indicating the presence of non-uniformity outlier. A feature is non-uniform outlier if its pixel noise exceeds a threshold established for a uniform feature. 1 indicates Feature is a non-uniformity outlier.
An RGlist with probes that are not non-uniformity Outlier (according to the correspondind AFE flag and the filtering options). It also writes an output file (IsFeatNonUnifOL.txt) that contains probes that were filtered out because they were considered non-uniformity Outlier.
Pedro Lopez-Romero
## Not run: data(dd) data(targets) library(hgug4112a.db) ddFILT=filter.NonUnifOL(dd,25,TRUE,targets,"hgug4112a.db") dim(ddFILT) ## End(Not run)