phipsonlab/speckle_old

R package for analysing single cell data

speckle_old's Issues

Fitting a mixed-effect model --> dream() instead of lmFit() or duplicateCorrelation()?

Hi,

Thanks for the clear explanations of your vignette!

I am interested in fitting a mixed-effect model (i.e., including the sequencing lane as a random effect). I noticed that in the 'More complex (or just different) experimental designs' section, you suggest to use lmFit() for LM, or duplicateCorrelation() for LMM, but I was wondering whether I could use dream() on the transformed proportions (props$TransformedProps of the vignette) since dream() can hold mixed-models and lmFit() not. See section 'Dream Analysis' for more details.

Thanks a lot!

Best,
Aida

Error with 2 levels clusters

Hello,

Thank you for this useful package.

When I provide a vector with 2 levels for the clusters argument in the propeller function, I get the following error :
Error in tmixture.matrix(out$t, stdev.unscaled, df.total, proportion, : Dims of tstat and stdev.unscaled don't match

Is it not possible to find differences of proportions when we only have 2 levels of cluster ?

FYI, I don't have any issue when the clusters argument has more than 2 levels and my study is based on the differences between 2 groups.

Thank you for your help.

Regards,
Yannick