RNAseq volcano plot of differentially expressed genes 

thank you for the nice video, I have a really naive and more mathematical question. what I have to define for pCutoff if I want to put the cutoff on padj value of 0.05? I mean the number that I'm definign for pcutoff should be already in -lo10(of the number) scale, or it shoud be the numer itself like 0.05 and it will be transforemd to -log10(x) Thank you in advance

Thank u for this helpful video ❤❤

What's the purpose of filtering by the basemean?

Thanks for this helpful video!

Thanks for taking up my suggestion. Good effort. How about the next step to be KEGG Pathway analysis .. Would be a logical conclusion to the entire series I believe.

Hi Mark. Would you please explain this? The raw count file name 'count' but why counts

Thanks so much for this excellent tutorial. I just want to confirm. In EnhancedVolcano, do we have to change the adjusted p value to the -log10 before running the command or should we use the adjusted p values directly like you did and the tool does the conversion? Because in your other video on making volcano plot using python, you calculated the -log10 of the adjusted p values before making the plot. I’m looking forward to your response. Many thanks!

Hello, If I do not want to present the gene symbol on the volcano plot, which option should I put? I do not want to do function of 'lab'.

Hi, I am trying to perform differential sequence analysis for an some data. I have completed up to featureCounts step. But I think my data is not ready for deseq2 step. Any recommendations on how to proceed? Thank you in advance.

Thank you for your tutorial. I have two questions: 1. What if the ENSEMBL does not have a corresponding SYMBOL? 2. If the p-value of one gene is very low, for example, Log10P = 100, then the volcano plot cannot show the high p-value genes since the y-axis is not enough to present them. How to deal with this?

Thank you for this tutorial! Would you please tell me how to output the plot in a square as you do? Because my output in R on Mac is in rectangle which made genes too condensed.

Thanks for your videos. I am using the DEseq for non model organism (sesamum indiucm), i am not able to match gene ids with map identifiers for enhanced volcano plot function. Please help me

Thanks

sir, what is this res.df?

you sound somehow like penguinz0

> EnhancedVolcano(res.df, x = "log2FoldChange", y = "padj", lab = res.df$symbol) Error in setup_params(...) : lazy-load database 'C:/Users/heonk/AppData/Local/R/win-library/4.3/gtable/R/gtable.rdb' is corrupt In addition: Warning message: In setup_params(...) : internal error -3 in R_decompress1