Hi there, thanks for the great tool. I have an experiment set up with three samples: 1).WT ctrl 2).gene X medium level knock down 3)gene X low level knock down. Each samples obtained from bone marrows from seperate mouses and are sequenced using 10x genomics scRNA seq protocol. I want to combine the raw count matrix of the three samples together and normalize across the three samples, but I saw in your vignette Section 3 SCnorm:multiple conditions:
In this step the assumption is that most genes are not differentially expressed (DE) between conditions and that any
systematic differences in expression across the majority of genes is due to technical biases
and should be removed.
I do expect knock down of gene x will cause gene expression changes which will have real biological indications in terms of differentiation/proliferation etc.. Does this mean SCnorm is not suited for my purposes? And more broadly speaking, is SCnorm suitable for normalize across samples in experiment set ups such as treatment vs control, gene knock down vs control etc? Thank you very much for your help!
Hi there, thanks for the great tool. I have an experiment set up with three samples: 1).WT ctrl 2).gene X medium level knock down 3)gene X low level knock down. Each samples obtained from bone marrows from seperate mouses and are sequenced using 10x genomics scRNA seq protocol. I want to combine the raw count matrix of the three samples together and normalize across the three samples, but I saw in your vignette Section 3 SCnorm:multiple conditions:
In this step the assumption is that most genes are not differentially expressed (DE) between conditions and that any
systematic differences in expression across the majority of genes is due to technical biases
and should be removed.
I do expect knock down of gene x will cause gene expression changes which will have real biological indications in terms of differentiation/proliferation etc.. Does this mean SCnorm is not suited for my purposes? And more broadly speaking, is SCnorm suitable for normalize across samples in experiment set ups such as treatment vs control, gene knock down vs control etc? Thank you very much for your help!