plotProbe: Plot probes

In maskBAD: Masking probes with binding affinity differences

Description

Pairwise plot probes of a probeset.

Usage

plotProbe(affy,probeset,probe=NA,probeXY=NA,scan=TRUE,ind,exmask="none",seqmask="none",names=FALSE)

Arguments

affy	An object of class AffyBatch.
probeset	Probe set name (Affymetrix ID).
probe	Number of the main probe.
probeXY	If probe is NA the x and y coordinates of the main probe can be given in the format 'x.y'.
scan	If scan is 'TRUE', each probewise comparison of the probe against all other probes in this probeset will be performed seperately. If scan is 'FALSE', all plots will be plotted in one layout. The layout has 3 columns. If the number of remaining probes that the probe should be compared with is not a multiple of 3, the number of probes will be reduced to the next lower multiple of 3.
ind	Numeric vector, with values 1 and 2, definining group assignement for samples in affy.
exmask	Optional: an expression mask object for this affy batch. Data frame with probe information, for example first element of the output of function mask. Should contain: column 1: probe x-coordinate, column 2:probe y coordinate, column 3: probeset, column 4: quality score: values to based filtering on, probes with values smaller than cutoff are discarded.
seqmask	Optional: a sequence mask object for this mask.
names	If 'TRUE' , the sample names are plotted to identify each individual.

Details

The function plotProbe plots single probe against all other probes of its probe set. The information from the expression based mask, the sequence based mask and the test for the two plotted probes is shown.

Author(s)

Michael Dannemann

References

Dannemann et al, The effects of probe binding affinity differences on gene expression measurements and how to deal with them. Bioinformatics 2009

See Also

mask, overlapExprExtMasks, prepareMaskedAffybatch

Examples

data(exmask)
data(AffyBatch)
## plot for one probe comparisons with other probes of the probeset
## for a random probeset
availableProbesets <- as.character(unique(exmask$probes[,4]))
availableProbesets
## scan the plots
## Not run: plotProbe(affy=newAffyBatch,probeset=availableProbesets[22],probe=5,scan=TRUE,ind=rep(1:2,each=10),exmask=exmask$probes,seqmask=sequenceMask)
## scan with names=TRUE
## Not run: plotProbe(affy=newAffyBatch,probeset=availableProbesets[22],probe=5,scan=TRUE,ind=rep(1:2,each=10),exmask=exmask$probes,seqmask=sequenceMask,names=TRUE)
## plot with given x y information
## Not run: plotProbe(affy=newAffyBatch,probeset=availableProbesets[22],probeXY="313.415",scan=TRUE,ind=rep(1:2,each=10),exmask=exmask$probes,seqmask=sequenceMask,names=TRUE)
## all plots in one layout
plotProbe(affy=newAffyBatch,probeset=availableProbesets[22],probe=5,scan=FALSE,ind=rep(1:2,each=10),exmask=exmask$probes,seqmask=sequenceMask)

maskBAD documentation built on Nov. 8, 2020, 5:15 p.m.