help. weird gene was detected as DEG
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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,

limma microarray • 352 views
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