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.
@sanbomics
2 жыл бұрын
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.
@saraalidadiani5881
11 ай бұрын
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
@waynejanuzaj9679
Жыл бұрын
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!
@sanbomics
Жыл бұрын
Hi! EhancedVolcano converts to -log10 automatically so you don't have to.
@waynejanuzaj9679
Жыл бұрын
Thank you so much! I appreciate it a lot.
@dorrarjaibi
10 ай бұрын
Thank u for this helpful video ❤❤
@chrisdoan3210
Жыл бұрын
Hi Mark. Would you please explain this? The raw count file name 'count' but why counts
@sanbomics
Жыл бұрын
In my case the raw file was named "count.out" not just "count". It shouldn't work if 'count.out' is changed to 'count'
@sanbomics
Жыл бұрын
Are you talking about my example, or your specific file? Sometimes the operating system may hide the extension
@chrisdoan3210
Жыл бұрын
@@sanbomics I got it. Thank you.
@mushtaqnajar8930
3 ай бұрын
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
@sanbomics
3 ай бұрын
You might have to parse the gtf file and get a dictionary from it
@BayAreaLakers
6 ай бұрын
What's the purpose of filtering by the basemean?
@snekhai
2 жыл бұрын
Thanks for this helpful video!
@sanbomics
2 жыл бұрын
Glad it was helpful!
@yijingwang7308
Жыл бұрын
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?
@sanbomics
Жыл бұрын
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.
@chrisdoan3210
Жыл бұрын
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.
@sanbomics
Жыл бұрын
if you save it like this you can adjust the width and heigh: kzitem.info/news/bejne/q4atyqWaqJGlhZw
@chrisdoan3210
Жыл бұрын
@@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.
@sanbomics
Жыл бұрын
I just clicked the pop-out button in the R studio output cell
@freezingtolerance7493
Жыл бұрын
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'.
@freezingtolerance7493
Жыл бұрын
And, based on the threshold that I set up, how can I calculate #genes that are upregulated or downregulated? always thank you
@sanjaisrao484
2 жыл бұрын
Thanks
@sanbomics
2 жыл бұрын
No problem!
@sekardeepika
2 жыл бұрын
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.
@sanbomics
2 жыл бұрын
You have a counts table? Thats all you really need for deseq2.
@thomas01pd2016
3 ай бұрын
> 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
@grace-426
Жыл бұрын
sir, what is this res.df?
@sanbomics
Жыл бұрын
It is just the deseq output results as a dataframe
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