weird entry in EnhanceVolcano Volcano plot -RNAseq

Question

[Yogesh]

Hi folks,

I am trying to plot volcano for one of my data. but i am getting some weird entry in one of the contrast analysis. can anyone help me understand why is this happening? Attaching the figure here. I have already checked my rownames, they are just fine. Plot Image is attached herewith

[MRezaei]

Hi. Could you share the script?

Answer 1

[weishengxin]

It's possible that the delimiter was not specified, which has resulted in the gene names becoming a combination of the name and a series of counts. You need to specify the delimiter, for example, when reading the input file, add sep=",", and also specify the columns required for plotting, which are typically three columns: name, log2fc, p or fdr.

[Yogesh]

Hi, Thank you for your response, I have specified the columns and separator both .

COUNTS <- as.matrix(read.table(file="normalized_G1.csv", sep=",", header=TRUE, row.names=1))
.
.
.
EnhancedVolcano(outputtable,
                 lab = rownames(outputtable),
                 x = 'log2FoldChange',
                 y = 'padj',pCutoff = 0.05,
                 FCcutoff = 1.5, maxoverlaps=70)

However, I can see some count entries in the file generated from dds2 contrast.

outputtable <- results(dds2, contrast=c("Group","Con", "treat"))
printed
"genes","baseMean","log2FoldChange","lfcSE","stat","pvalue","padj"
"DHHC30",377.012272028959,0.474098461761811,0.169483994907806,2.79730520878804,0.0051530829406312,0.0147856101044728
"DU3",883.22947623877,0.473611221694096,0.102809617601126,4.60668206676519,4.09144834245092e-06,2.33550176012568e-05
"PP2A-BBETA,903,692,480,354,100,101,162,166,508,279,383,303,64,113,20,52,391,373,346,432,579,421,300,140,545,295,592,217,168,129,346,189
MFS1,0,1,0,0,0,0,0,2,11,0,11,2,0,3,0,0,0,0,0,0,0,1,0,1,1,9,0,5,0,0,1,2
AGO12,3,0,3,1,0,1,2,0,2,0,1,0,0,0,0,0,1,0,0,0,4,0,1,0,0,0,0,0,0,0,0,0
AGO11,0,0,4,1,0,0,0,0,0,0,2,0,1,7,0,0,198,154,255,319,75,48,162,150,732,453,578,184,52,50,129,81

[1769mkc]

you can use dput for the dataframe and add he same in your question instead of putting as new answer.

[Yogesh]

hi Thank you for your guidance. turned out that my gene names have special characters which are throwing these errors