Running mfisthtools with no 'off' clusters

AllenInstitute / mfishtools

Building Gene Sets and Mapping mFISH Data

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Running mfisthtools with no 'off' clusters #2

Closed AlexanderAivazidis closed 5 years ago

AlexanderAivazidis commented 5 years ago

Hi!

I am trying to run mfishtools with no 'off' clusters and I get no genes back from the filterPanelGenes function. I think it might be related to the 'maxOff' parameter that is by default set to 50. In line 218 of your code you set the constraint maxExprOff<=maxOff But before that in line 203 you set maxExprOff <- maxExprOn*Inf, for the case that there are no off clusters. Is there a minus missing?

Thanks

Alexander

jeremymiller commented 5 years ago

Hi Alexander! Thanks for pointing this out. It should be fixed now. Sorry for the delay at getting back to you--I didn't receive a notification about this issue and forgot to check.
Best, Jeremy