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bvieth avatar bvieth commented on June 3, 2024

Hello,

thank you for trying out powsimR!

scater changed its parameters for QC quality metrics. I have adapted my function call accordingly in the newest version (1.1.2). Feel free to give it another go and please tell me if you encounter other issues.

Kind regards
Beate

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abrantesas avatar abrantesas commented on June 3, 2024

Great it works now! Although I think powsimR no longer loads the scater package.
I get this error when running the simulateDE function:

Applying MAST for DE analysis on raw count data.
Error in assayNames(x) : could not find function "assayNames"

If I load library(scater) it works fine.
Thanks again. Feel free to close the issue.

Shawn

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bvieth avatar bvieth commented on June 3, 2024

Hello Shawn,

great to here!

Concerning the error message for MAST, can you send me the output of your sessionInfo() after library(powsimR)? I actually never used a call to assayNames nor scater in my wrapper for DE detection with MAST.
Which version of MAST and R do you have? I am on 1.4.1 for MAST and still 3.4.4 for R.

Kind regards
Beate

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abrantesas avatar abrantesas commented on June 3, 2024

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