Entering edit mode
2.4 years ago
Aki
▴
20
hello I'm trying to analyze microarray data (affymetrix.genechip.hg-u133_plus_2). I have detected much of DEG log(FC)>1, but some of DEG seem to have small changes. normalized value (RMA) of one gene which was detected as DEG is shown below.
CTRL_1 CTRL_2 CTRL_3 CTRL_4 CTRL_5 treat_1 treat_2 treat_3 treat_4 treat_5
2.369982 2.091826 2.117409 2.332377 2.311217 2.332377 2.552579 2.550049 2.150150 2.464459
Isn't there something wrong I did? or this is normal? this is my code.
group_1 <- c(1:10)
data <- read.table(in_f2, header=TRUE, row.names=1, sep="\t", quote="")
data_1 <- data[,group_1]
design_1 <- model.matrix(~ pairinfo+group_list_1)
fit_1 <- lmFit(data_1,design_1)
fit_1 <- eBayes(fit_1)
DEG_1 <- topTable(fit_1, adjust = 'BH',coef = 6, number = Inf, p.value = 0.05, lfc = 1)
regards,