Question: DESeq2 Log2 Fold Change values do not match up between my Rank List and my MA Plot
gravatar for ejmcmaho
4.4 years ago by
United States
ejmcmaho0 wrote:


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 =[order(abs(results$log2FoldChange), decreasing=T),])
head(rankList, n=15)

# MA plot
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(,baseMean > 1000)
high_exp = high_exp[order(high_exp$baseMean, decreasing=T),]

Any guidance would be much appreciated.

Thank you,


deseq2 rna-seq • 1.1k views
ADD COMMENTlink modified 4.4 years ago by Dario Strbenac1.5k • written 4.4 years ago by ejmcmaho0

i'm not sure what could be going on. you are saying when you order the results table by LFC and when you plot the LFC the values are different?

ADD REPLYlink written 4.4 years ago by Michael Love26k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 194 users visited in the last hour