I would like to ask everyone some questions.
I am doing a genome wide screening of siRNA.
At the end of data analysis, I manage to generate the correct data but fail to annotate the wells.
Even though the state is TRUE for annotation but they are not in html report.
x <- readPlateList("platelist.txt", name = expName, path=dataPath)
x<-configure(x,confFile = confFile, logFile = logFile,descripFile = desFile, path = dataPath)
xn<-summarizeChannels(x,fun = function (r1,r2,r3,r4,r5,r6,r7) r5/r3)
xnp <- normalizePlates(xn, scale = "multiplicative", log = TRUE, method = "negatives", varianceAdjust = "none")
xsc <- scoreReplicates(xnp, sign = "+", method = "zscore")
xf <- summarizeReplicates(xsc, summary = "mean")
I tried to annotate the x (raw) and xf (summarized) one, but they generated the same results.
Plate Well GeneID
1 A01 DMPK
1 A02 empty
1 A03 TTK
1 A04 PIK3CA
1 A05 SYK
1 A06 KIAA1804
1 A07 EPHA8
1 A08 NAGK
1 A09 empty
1 A10 IRAK1
Please someone help me with this.