No differentially expressed genes

Hi,

I have a dataset now with 36k lncRNAs and I’m using DESeq2 to find differentially expressed lncRNAs between a healthy group and a disease group, but unfortunately I cannot find any DE lncRNAs with low padj values. However, when I explore my data by taking the log2 fold change of the mean gene counts of the disease group subjects and divide this by the mean gene counts of the healthy group, the log2 fold change is >2 or <-2 for some genes, which to me would imply that some genes should be differentially expressed. Also, what is strange to me, is that the samples from the same group do not cluster together well.

To make things clear I have written the formula for the FC below:
log2(mean gene counts for a certain gene in disease group) / mean gene counts for a certain gene in healthy group).
Also, I have added a picture of a histogram with the fold changes and a PCA plot.

Lastly, this is the code that I used for DESeq2:

dds<-DESeqDataSetFromMatrix(df,colData = 
metadata,design = ~design)
dds<-estimateSizeFactors(dds)
ddsnormalized<-counts(dds,normalized=TRUE)
vsdlncrna<-vst(dds,blind=TRUE)
plotPCA(vsdlncrna,intgroup="design")
dds<-DESeqDataSetFromMatrix(df,colData = metadata,design = ~design)
dds<-DESeq(dds)
results(dds,contrast = c("design","cancer","healthy"))
lncrnares<-results(dds,contrast = c("design","cancer","healthy"),alpha = 0.05)

Does anyone know if I made a mistake here?
Thanks in advance!

fold change picture with frequency of genes with certain fold changes

PCA plot of cancer and healthy group

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