The volcano plot shows data with an arm-shaped enrichment.
Hi. I analysed my Transcriptomics data as followed: Trimmomatic, Kallisto, R: tximport,
> dge <- DGEList(counts = txi$counts)
> colnames(dge) <- sample_names
> keep <- rowSums(cpm(dge) > 1) >=3
> dge <- dge[keep, , keep.lib.sizes = FALSE]
> dge <- calcNormFactors(dge, method = "upperquartile")
> norm_counts <- cpm(dge,normalized.lib.sizes = TRUE)
In the end, I visualised the data in a volcano plot, which looks like this:
Unfortunately, I don't know what happened to the data that it has such a structure, why it forms such an arm-shaped accumulation. If you know of any reasons for the enrichment or possible solutions, I would be grateful.
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Usually odd shapes in these sorts of plots come from insufficient prefiltering. Here, in your
keepall you do is to make sure that the genes is not all-zero, it is not group-aware. I would recommendfilterByExpr()as suggested in the edgeR user guide.