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feiyoung / PRECAST

an efficient data integration method for multiple spatial transcriptomics data with non- cluster-relevant effects such as the complex batch effects.
GNU General Public License v3.0
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Error when running IntegrateSpaData #10

Closed agelber-ucsd closed 1 year ago

agelber-ucsd commented 1 year ago

Hi,

I am trying to run IntegrateSpaData and after downloading the newest version to be able to include biological covariates I am getting the following error.:

Error in [[<-.data.frame(*tmp*, i, value = c(1084623L, 5715162L, 1110488L, : replacement has 8768019 rows, data has 224821

Any idea why this my be happening? It happens at this line:

hX <- get_correct_exp(XList, PRECASTObj@resList$Rf, houseKeep = houseKeep, q_unwanted = min(10, length(houseKeep)), covariateList = covariateList)

It works without the covariates included but once included I get the error above.

-Alon

Update: I'm not sure if you're also seeing this error but I'm getting it at the linear model step: lm1 <- lm(X0 ~ 0 + cbind(M0, Rf))

feiyoung commented 1 year ago

Thank you for bringing this bug to our attention. We are pleased to inform you that it has been resolved in the development version of PRECAST on GitHub (PRECAST version 1.6.1). We appreciate your valuable contribution towards enhancing PRECAST, and thank you once again!

agelber-ucsd commented 1 year ago

Thanks! I realized later it had something to with factor types in the model but I'll just go ahead and install the development version. Thanks again for your prompt response!