Thank you for your excellent videos-they’ve been incredibly helpful! I have a question regarding my experiment. I have two groups, and each group contains three mixed samples. I would like to compare these groups and create a volcano plot. However, since my samples are mixed, I'm unsure how to proceed with calculating p-values. Is it still possible to create a volcano plot under these conditions? Any guidance would be greatly appreciated.
Hi - thank you so much for your feedback! I guess there's not many limitations as to creating a volcano plots to compare groups. The question is more - what do you want to answer/find? Does it make sense to group samples together? If you'd like to give me more details I might be able to give you more specific feedback:)
@@biostatsquid Hi thanks for your reply! Actually I have two groups, test and control. each of them has tumor samples of three mice which became mixed and then single cell analysis were done on them, so although there are three samples in each group, but I don't have p value for each group. could toy please tell me how can I have a volcano plot? thanks! And one more asking could you please teach Azimuth for annotation please?
Thanks for your comment, of course! Coming up in my next videos, but you can already find the code here: biostatsquid.com/scdblfinder-tutorial/ Essentially you just use the "subset" function from Seurat. seu_dblt
You can find the step-by-step tutorial here: biostatsquid.com/scdblfinder-tutorial/
Thank you for your excellent videos-they’ve been incredibly helpful! I have a question regarding my experiment. I have two groups, and each group contains three mixed samples. I would like to compare these groups and create a volcano plot. However, since my samples are mixed, I'm unsure how to proceed with calculating p-values. Is it still possible to create a volcano plot under these conditions? Any guidance would be greatly appreciated.
Hi - thank you so much for your feedback! I guess there's not many limitations as to creating a volcano plots to compare groups. The question is more - what do you want to answer/find? Does it make sense to group samples together? If you'd like to give me more details I might be able to give you more specific feedback:)
@@biostatsquid Hi thanks for your reply! Actually I have two groups, test and control. each of them has tumor samples of three mice which became mixed and then single cell analysis were done on them, so although there are three samples in each group, but I don't have p value for each group. could toy please tell me how can I have a volcano plot? thanks!
And one more asking could you please teach Azimuth for annotation please?
Hi, could you please tell me how can we exclude these doublets from analysis?
Thanks for your comment, of course! Coming up in my next videos, but you can already find the code here:
biostatsquid.com/scdblfinder-tutorial/
Essentially you just use the "subset" function from Seurat.
seu_dblt
@@biostatsquid Thanks a lot! I am very eager for upcoming videos!