I have the an annotated dataframe which contain the results of my Differential gene expression using Deseq2: I used this data frame for volcano plot where I got the gene that I have activated with -log10p-value = 200, I had to do some specification and coloring for some genes and so I have filtered my targeted genes from the same dataframe extracting the whole rows and I have plotted them again to get the same gene plotted in -log10P-value =40, Y axis was listed from FDR I looked up the FDR value of the same gene it was 0.0000000000, I tried to export the dataframe to excel it was 0.000000000000e+00 here I list the code

volcanoplot of all results from shrink.tab dataframe all genes of DGE

EnhancedVolcano(shrink.tab, x='logFC', lab = shrink.tab$Symbol,
                y= 'FDR', title = 'TG Vs WT wnt1 Volcano plot', 
                subtitle = 'differentially expressed genes',
                pCutoff = 0.05,
                FCcutoff = 1)

here I got a results where -log10Pvalue = 200

Sigsymb <- shrink.tab %>% dplyr::filter(grepl('Wnt|Dvl|Dkk1|Dkk2|Dkk3|Fzd|Lrp5|Lrp6|Axin|Ctnnb1', Symbol))
Sigsymb.l <- shrink.tab %>% dplyr::filter(grepl('Wnt|Dkk1|Dkk2|Dkk3', Symbol))%>% pull(Symbol)
Sigsymb.r <- shrink.tab %>% dplyr::filter(grepl('Fzd|Lrp5|Lrp6', Symbol))%>% pull(Symbol)
Sigsymb.s <- shrink.tab %>% dplyr::filter(grepl('Dvl|Axin|Ctnnb1', Symbol))%>% pull(Symbol)

keyvals.colour <- ifelse(Sigsymb$Symbol %in% Sigsymb.l , 'royalblue',
                         ifelse(Sigsymb$Symbol %in% Sigsymb.r, 'gold',
                                'darkred'))

keyvals.colour[is.na(keyvals.colour)] <- 'darkred'
names(keyvals.colour)[keyvals.colour == 'gold'] <-'receptors'
names(keyvals.colour)[keyvals.colour == 'darkred'] <- 'signaling protein'
names(keyvals.colour)[keyvals.colour == 'royalblue'] <-  'ligands'

EnhancedVolcano(Sigsymb, x='logFC', 
                lab = Sigsymb$Symbol[which(names(keyvals.colour) %in% c('receptors', 'ligands','signaling protein'))], 
                labSize = 6.0, colCustom = keyvals.colour,
                colAlpha = 1,
                legendPosition = 'right',
                legendLabSize = 16,
                legendIconSize = 4.0,
                drawConnectors = TRUE,
                y= 'FDR', title = 'TG Vs WT wnt1 Volcano plot', 
                subtitle = 'differentially expressed genes',
                pCutoff = 0.05, FCcutoff = 0) 

here I got the results where -log10Pvalue = 40

Could you please explain if there's any error during coding and if not what might be an explanation to what happened?

thank you in advance!

Hi,

It's likely related to the following fact: some differential expression analysis programs in the R framework output p-values of 0, but these cannot be converted via -log10. Therefore, in EnhancedVolcano, I programmed it so that these p-values are converted to 10^-1 x the lowest non-zero p-value. Thus, if we have this situation:

• EGFR, p=0

• BRCA1, p=0.0001

, EGFR's p-value will be converted to 0.0001 * 10^-1 = 0.00001, prior to plotting.

The code in question is here: https://github.com/kevinblighe/EnhancedVolcano/blob/master/R/EnhancedVolcano.R#L321-L334

Kevin