Hello everyone, I am working on scRNA-Seq data analysis. I mainly focused on Scater and Seurat. For some visual properties I (and my PI) want to use Seurat too but it only has LogNormalization. I believe it just takes the logarithm (in Seurat it is natural log not log2 I think).
I want to use deconvolution method which is provided by Scater package. Convert() function of Seurat transforms a SingleCellExperiment to Seurat Object but I think I causes the loss of some metadata.
I used Seurat until normalisation and converted it to SingleCellExperiment object, normalised it (without transforming values to log). What should I do now? I can convert the SingleCellExperiment object to Seurat object, log normalize it and keep going as in tutorial (I am not sure how scaling factor effects). As another option, I can change only data matrix (seuratdata@data and exprs/normcounts(singlecellobject).
Is there a simple way to do it?
Thank you all.