Hi there, Would it be possible to clarify how the PLATE-Seq gene expression values were obtained? I thought PLATE-Seq would produce read counts, but the values are continuous, so it seems taht some kind of data processing was involved. Thanks in Advance, Andrea

Created by Andrea Degasperi andrea.degasperi
Hi @efd2115 , is there any reason why the raw counts were normalized? I think raw counts might be more useful for some models. Is it possible to share the raw counts as well? Best, Alberto
So first of all the PlateSeq method involves 3' sequencing (not whole transcript) and so the effect of transcript size is taken care of by the technology. From the counts processing stand point the expression normalization procedure is: 1. Quantile Normalization 2. Variance Stabilization 3. Batch correction of Plates with ComBat
cc @efd2115

PLATE-Seq gene expression values page is loading…