First I'd like to thank you for this wonderful tool that helped me a lot with RNAseq analysis ! I am currently running some analysis on scRNAseq data which are king of messed up by the batch effects.
I have used CombatSeq to correct for the batch on the pseudo-bulk count but I was wondering whether a similar approach could be used on the raw single cell count instead of the pseudobulk matrices ?
I found an adaptation on the singleCellTK for scRNAseq but with my large dataset it keeps crashing probably because it tries to create a matrix from my very large SCE object.
Do you have experiences this type of analysis on scRNAseq ? Is this something doable to you ?
Hi,
First I'd like to thank you for this wonderful tool that helped me a lot with RNAseq analysis ! I am currently running some analysis on scRNAseq data which are king of messed up by the batch effects. I have used CombatSeq to correct for the batch on the pseudo-bulk count but I was wondering whether a similar approach could be used on the raw single cell count instead of the pseudobulk matrices ? I found an adaptation on the singleCellTK for scRNAseq but with my large dataset it keeps crashing probably because it tries to create a matrix from my very large SCE object. Do you have experiences this type of analysis on scRNAseq ? Is this something doable to you ?
Many thanks for the insights !
Alll the best,
Salim.