Question: EnhancedVolcano with gene names
0
gravatar for mannoulag1
24 months ago by
mannoulag160
mannoulag160 wrote:

Hi, I used EnhancedVolcano to obtain a nice volcano plot but I need the gene names in the figure not the gene ID, tt is the result of toptable, Thank you

tt<-topTable(fit2, adjust="fdr", number=Inf)
EnhancedVolcano(tt,lab = rownames(tt),x = "logFC",
y = "adj.P.Val",pCutoff = 0.05,FCcutoff = 2,transcriptPointSize = 1.5,
ylab = bquote(~-Log[10]~adjusted~italic(P)), legend=c("NS","Log2 FC","Adjusted p-value","Adjusted p-value & Log2 FC"),
 transcriptLabSize = 3.0, title= ".........")
limma enhancedvolcano R • 1.3k views
ADD COMMENTlink written 24 months ago by mannoulag160
1
gravatar for Kevin Blighe
24 months ago by
Kevin Blighe65k
Kevin Blighe65k wrote:

Hi, I developed EnhancedVolcano. What are your gene IDs, currently? Can you paste them? You may need to convert them via biomaRt.

ADD COMMENTlink written 24 months ago by Kevin Blighe65k

Hi Kevin, yes thank you very much for providing EnhancedVolcano, I am very interested to use it :) I succeeded to obtain the gene symbols from biomart, so I have ensemble_gene_id and the symbols but how can I use this in lab attribute? thank you

ADD REPLYlink modified 24 months ago • written 24 months ago by mannoulag160

Good work, dude!

ADD REPLYlink written 24 months ago by Kevin Blighe65k

how can I use this in lab attribute? thank you

ADD REPLYlink written 24 months ago by mannoulag160
1

Ah, you edited your comment. I thought that you had the new labels already. Have you produced a lookup table from biomaRt?

I perform matching between biomaRt output and Affymetrix IDs, here: C: Annotate Affymetrix probesets to Gene symbols

Perhaps you can follow that in order to matching your Ensembl IDs to HGNC IDs.

ADD REPLYlink written 24 months ago by Kevin Blighe65k
1

perfect !!! Thank you kevin

ADD REPLYlink written 24 months ago by mannoulag160
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