Dear all,
I know that SEURAT is not a BioC package, and if I may have your permission to post the question here, hoping to have your insights ;)
After following the tutorial that is available at : https://satijalab.org/seurat/immune_alignment.html, the questions would be :
1 -- after running " immune.combined <- RunCCA(ctrl, stim, genes.use = genes.use, num.cc = 30)"
in @data and @scale.data, we have the normalized data and the scaled data of the samples as available in the objects "ctrl.data", and "stim.data", correct ? Or, were these data modified by CCA algorithm ?
2 -- I could see that the command :
"immune.combined <- AlignSubspace(immune.combined, reduction.type = "cca", grouping.var = "stim", dims.align = 1:20)"
changes only the @scale.data. and not the normalized values in @data : is this a correct observation, and is it expected ?
in which slot of "mmune.combined " could i find the corrected/CCA-aligned "normalized data" of those 2 samples ?
thanks a lot !
-- bogdan
Just in case that there is someone else asking the same question, 've found the answer here :
"https://github.com/satijalab/seurat/issues/283", where the authors said an year ago that --
"Seurat does not return batch-corrected expression values (if we did, we would not be able to compare expression values over different conditions, as these would be subtracted). Instead, Seurat can be used to generate a corrected cell/cell distance matrix."