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Meta regression steps and Error #191
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I don't know if this package is still being maintained but I found the error and also another error that came up. The first which was the topic of the post was caused by the one_ct_genes call within CSIDE.population.inference not also subseting the design matrix with the present celltypes (change parameter from meta.design.matrix to meta.design.matrix[ct_pres,]). A different error then appeared in the get_de_pop and get_means_sds functions where the ct_ind celltype index takes the index from the first sample only, when the index is different for every sample. I attached my modified functions below. Hopefully I didn't introduce any new errors.
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Hi,
I'm trying to use the CSIDE.population.inference function to perform meta regression. I have a batch variable and a group variable and want to control for the batch while testing differences in the group.
I first ran RCTD
Next, I ran run.CSIDE.intercept for each sample in the myRCTD.reps object so that I could later test only by group, following the suggestion from here #145
Finally, I attempted to run the meta regression, but am getting a runtime error halfway through this step.
I was wondering if you could confirm if these are the right steps for what I'm trying to do, and if so how I could fix this error. Thank you
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