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GabrielHoffman / dreamlet

Perform differential expression analysis on multi-sample single cell datasets using linear mixed models
https://gabrielhoffman.github.io/dreamlet
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Multiple treatment groups #21

Open jindalk opened 4 months ago

jindalk commented 4 months ago

Hi, I am trying to use dreamlet for a dataset with one control and multiple treatment groups per cell type. I wish to compare each treatment group to the same control group. In some other tools, this is achieved by converting the treatment column in the metadata to a factor and setting "Control" as the first level.

Does dreamlet follow a similar behavior?

Thanks, Kunal

GabrielHoffman commented 4 months ago

Any study design that will work for limma will also work in dreamlet. But you say 'dataset with one control', and limma/dreamlet, etc are only applicable when there is variation within each group. With only one control, there is no way to estimate the variance within the control group, so a regression approach won't work.

jindalk commented 4 months ago

Ah sorry for the confusion. I meant to say my data is grouped into three categories "Treatment 1", "Treatment 2", and "Control", each of them contain multiple samples.