Hello all,
I want to ask a question about Log2FoldChange in DESeq2. In many cases for the similar counts of Case and Control if the count shows down regulation but the DESeq2 give the output Up regulation, it gives us trouble for further analysis, so can anybody tell me how to deal with this problem.
here is some sample of our data.
GENES | logfc | adjpv | Counts_Control | Counts_Case |
xyz1 | 2.000605 | 0.000001 | 2231 | 1330 |
xyz2 | 2.001338 | 0.000001 | 290 | 173 |
xyz3 | 2.012326 | 0.000001 | 92 | 55 |
xyz4 | 2.005319 | 0.000001 | 433 | 259 |
xyz5 | 2.012833 | 0.000001 | 75 | 45 |
xyz6 | 2.006388 | 0.000001 | 30 | 18 |
xyz7 | -2.34172 | 0.000001 | 2111 | 62 |
xyz8 | -2.34066 | 0.000001 | 1225 | 36 |
xyz9 | -2.33344 | 0.000001 | 238 | 7 |
xyz10 | -2.33951 | 0.000001 | 1768 | 52 |
as you can see in above table xyz1-xyz6 results are Down Regulated but the DESeq2 give the Up Regulation.
where xyz7-xyz10 shows the correct result. Please help me in this problem.
Waiting for positive response.
Thank you for reply,
====================================================================
library(DESeq2)
directory<-"/home/projects_110_AmpliseqRNA/all_samples_with-replicates/LN_R2"
sampleFiles <- grep("treated",list.files(directory),value=TRUE)
sampleCondition<-c("treated","treated","treated","untreated","untreated","untreated")
sampleTable<-data.frame(sampleName=sampleFiles, fileName=sampleFiles, condition=sampleCondition)
sampleTable
ddsHTSeq<-DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory=directory, design=~condition)
colData(ddsHTSeq)$condition<-factor(colData(ddsHTSeq)$condition, levels=c("untreated","treated"))
dds<-DESeq(ddsHTSeq,fitType="mean")
res<-results(dds)
res<-res[order(res$padj),]
head(res)
mcols(res,use.names=TRUE)
write.csv(as.data.frame(res),file="Raw_File_deseq2.csv")
FileforIpathway=res[,c(2,6)]
write.csv(as.data.frame(FileforIpathway),file="File_deseq2.csv")
pdf("DEseq2_MA_plot.pdf")
plotMA(dds,ylim=c(-10,10),main="DESeq2")
dev.off()
pdf("DESeq2_Dispersion_plot.pdf")
plotDispEsts(dds)
dev.off()
====================================================================
This is the code which i am using for analysis.