-
Notifications
You must be signed in to change notification settings - Fork 14
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Are logcounts required in sce object? #13
Comments
Hi @catsargent Only raw counts are necessary if you run the DE analysis and wrapper with default parameters ( Can you provide your exact error message when running About the wrapper: one of the functions in the wrapper |
Hi, Sorry for the delay in responding - I was on holiday. This is the error I obtain when run get_DE_info using the step-wise approach and my object does not contain log normalized counts. But from your previous message, it sounds like I would need to have log normalized counts in the object and therefore the error would be expected if they are not found? Thanks,
|
Hi @catsargent |
You're right - you had suggested using that option when troubleshooting the error in another issue (#7) and I did not change it back. Thank you! |
OK, thanks for letting me know. |
Hi,
Please can you confirm whether the count data needs to be log normalized or not in the sce object? In step-by-step mode, when I run get_DE_info on my data it gives an error about not finding logcounts in the assay slot.
However, when I run the wrapper function on that same data, the DE analysis part works (it later fails when reaching the "Combine all the information in prioritization tables" section (I created an issue on github for this). I just wanted to check with you why the wrapper function does not fail if there are not logcounts in the assay slot. Are these somehow generated if using the wrapper script?
Thanks,
Catherine
The text was updated successfully, but these errors were encountered: