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
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.
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!
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?
These are both dealer's choice. I would keep the ensembl id and put that instead. You can either put a maximum value on your chart (ie if the value is 97 make it 10, just make sure to say this in legend) or do a broken axis.
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
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.
> 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
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Thank u for this helpful video ❤❤
Thanks for this helpful video!
Glad it was helpful!
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
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.
Thanks for another suggestion. It's a good idea. In the meantime, I do show KEGG enrichment in my DAVID video. Its not in R but still useful.
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!
Hi! EhancedVolcano converts to -log10 automatically so you don't have to.
Thank you so much! I appreciate it a lot.
Thanks
No problem!
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?
These are both dealer's choice. I would keep the ensembl id and put that instead. You can either put a maximum value on your chart (ie if the value is 97 make it 10, just make sure to say this in legend) or do a broken axis.
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.
if you save it like this you can adjust the width and heigh:
ruclips.net/video/JPwdqdo_tRg/видео.html
@@sanbomics Thank Mark. I didn't see you use png function in this video, just drag the plot from somewhere I don't know how you get it.
I just clicked the pop-out button in the R studio output cell
Hi Mark. Would you please explain this? The raw count file name 'count' but why counts
In my case the raw file was named "count.out" not just "count". It shouldn't work if 'count.out' is changed to 'count'
Are you talking about my example, or your specific file? Sometimes the operating system may hide the extension
@@sanbomics I got it. Thank you.
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
You might have to parse the gtf file and get a dictionary from it
What's the purpose of filtering by the basemean?
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'.
And, based on the threshold that I set up, how can I calculate #genes that are upregulated or downregulated? always thank you
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.
You have a counts table? Thats all you really need for deseq2.
sir, what is this res.df?
It is just the deseq output results as a dataframe
you sound somehow like penguinz0
Haha I'll take that as a compliment xD
> 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