Help! Volcano plot in R with seurat and ggplot #6674
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scRNAseqnovice
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See Seurat's DEG vignette: https://satijalab.org/seurat/articles/de_vignette.html It sounds like you want to compare within a cell cluster, between cells from before and after treatment. The general process for detecting genes then would be:
Repeat for all cell clusters/types of interest, depending on your research questions. |
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Hi, I am a novice in analyzing scRNAseq data. I have been following the Satija lab tutorials and have found them intuitive and useful so far.
I would like to create a volcano plot to compare differentially expressed genes (DEGs) across two samples- a "before" and "after" treatment.
I have scoured the web but I still cannot figure out how to do this.
I have successfully installed ggplot, normalized my datasets, merged the datasets, etc., but what I do not understand is how to transfer the sequencing data to the ggplot function. I keep receiving an error that says:
"data must be a <data.frame>, or an object coercible by fortify(), not an S4 object with class ."
I have seen tutorials on the web, but the data there is not processed the same as how I have been doing following the Satija lab method, and, my files are not .csv, but instead are .tsv
Any tips would be appreciated!
Thanks!
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