Hashtags in volcano plots

hi, I have two treatments, each treatment has 3 hashtags.
I want to compare the two treatments and create a volcano plot. However, when you ignore the hashtag, it just thinks there is 1 sample for each treatment. I have separated the hashtags, and loaded the 3 files for each hashtag +treatment. However, I can’t get the correct comparison for the volcano plot.

anyway here that has used hashtags successfully t

Hi Julie, thanks for your question. To effectively compare two treatments, each with three samples (hashtags), you indeed need to check that all six samples appear in the Data Management module. Here you should add a new metadata column, named, for example, “treatments,” where you assign the respective treatment labels to each sample.

Once you have properly organized and processed your data, you can proceed to create the volcano plot. When generating the plot, ensure that you select the option “Compare a selected cell set between samples/groups.” This selection will allow you to specify the treatment labels in the dropdown menus labeled “between sample/group” and “and sample/group.”

By following these steps, you should be able to compare the two treatments and create your volcano plot. I hope I understood your question correctly. If you have any further questions or encounter any issues, feel free to let me know.