| backgroundChannelSubtract {blima} | R Documentation |
Function to subtract one channel from another producing new channel. Standard graphic subtraction.
backgroundChannelSubtract(b, normalizationMod = NULL, channelSubtractFrom = "GrnF",
channelSubtractWhat = "GrnB", channelResult = "Grn")
b |
List of beadLevelData objects (or single object). |
normalizationMod |
NULL for performing on all input b. Otherwise specifies logical vector of the length equals to the number of arrays in b or list of such vectors if b is a list of beadLevelData classes. |
channelSubtractFrom |
Name of channel to subtract from. |
channelSubtractWhat |
Name of channel to subtract. |
channelResult |
Result channel, if this channel exists it will be overwritten. |
Vojtěch Kulvait
if(require("blimaTestingData") && interactive())
{
#To perform background correction on blimatesting object for two groups. Background correction is followed by correction for non positive data. Array spots out of selected groups will not be processed.
data(blimatesting)
#Prepare logical vectors corresponding to conditions A and E.
groups1 = "A";
groups2 = "E";
sampleNames = list()
c = list()
for(i in 1:length(blimatesting))
{
p = pData(blimatesting[[i]]@experimentData$phenoData)
c[[i]] = p$Group %in% c(groups1, groups2);
sampleNames[[i]] = p$Name
}
#Background correction and quantile normalization followed by testing including log2TransformPositive transformation.
blimatesting = bacgroundCorrect(blimatesting, normalizationMod=c, channelBackgroundFilter="bgf")
blimatesting = nonPositiveCorrect(blimatesting, normalizationMod=c, channelCorrect="GrnF", channelBackgroundFilter="bgf", channelAndVector="bgf")
}else
{
print("To run this example, please install blimaTestingData package from bioconductor by running BiocManager::install('blimaTestingData').");
}