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kevinblighe / EnhancedVolcano

Publication-ready volcano plots with enhanced colouring and labeling
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Weird enhanced volcano plot after performing LFCshrinage #68

Closed cannico30 closed 3 years ago

cannico30 commented 3 years ago

Hi everyone, I used the TCGA database for melanoma to perform DEseq2 analysis. After I performed the lfcshrinkage command, my enhanced volcano plot looks very weird.

Does anybody have an idea?

Thank you very much in advance. the first plot is performed without lfc shrinkage and the second one with. volcano plot without lfc

volcano plot after lfcs

kevinblighe commented 3 years ago

Hi, I think that this is more of an issue with the lfc shrinkage method of DESeq2. Sorry. You may want to post on the Bioconductor Support forum, but first search for previous similar questions.

Kind regards, Kevin

cannico30 commented 3 years ago

Hi Kevin,

thank you very much for your answer. I do have another question: What is the default setting for the volcano plots to assume the fold change is 0? Because when I look in my data output the fold change is never 0, it is just very small.

Best wishes,

Nico