Hi,

I am attempting to do a differential expression analysis comparing one organism supplemented with bacteria and another that is not. When looking at my MA Plot it appears that there are man genes that have a log2 fold change > 2 , in my rank it shows that there are only 11 such genes. Has anyone else experienced this problem? Here is my code for both the rank list and MA plot if that is helpful: 

# order by Fold Change - Rank List
rankList = as.data.frame(results[order(abs(results$log2FoldChange), decreasing=T),])
head(rankList, n=15)

# MA plot
options(scipen=1)
plotMA(results, main="BF vs SUP MA Plot", ylim=c(-15.0, 15.0), colSig='green2', cex=0.6)
plot(results$log2FoldChange ~ results$baseMean,log='x', ylab="log2 Fold Change", xlab="Mean Expression", pch=16, cex=0.6, col="gray32", main="BF vs SUP MA Plot")
abline(h=0, col='red')
points(results$log2FoldChange[sigGenesFCpval] ~ results$baseMean[sigGenesFCpval], col = "green2", pch = 16, cex=0.7)

high_exp = subset(as.data.frame(results),baseMean > 1000)
high_exp = high_exp[order(high_exp$baseMean, decreasing=T),]
high_exp

Any guidance would be much appreciated.

Thank you,

Evan