compare multiple pairs concurrently

[pchiang5]

Hi,

My dataset contains single-cell data with the following 6 treatments:

A
A+B
A+B+C
A+C
A+C+D
A+B+C+D

I would like to know the genes specifically induced by B. I wonder if it is okay and more robust to perform pairwise comparisons as below and get the aggregated output of significant genes induced by B in all conditions?
A vs A+B
A+C vs A+C+B
A+C+D vs A+C+D+B

Thanks!

[const-ae]

Hi,

I wonder if it is okay and more robust [...]

'More' compared with what?

A vs A+B
A+C vs A+C+B
A+C+D vs A+C+D+B

All these three comparisons are equal to just testing for the effect of B (assuming you have a one-hot encoding for your conditions).

Best,
Constantin

[pchiang5]

Hi Constantin, My concern is including C in the 2nd group and C&D in the 3rd group might lead to the presence of different sets of differential expressing genes. By pseudobulking the 3 pairs as separate conditions, is it possible to get a more consistent (robust, regardless the confounding 'irrelevant' factors) ones responding to +B? Best, Po

…

On Tuesday, November 15, 2022, Constantin ***@***.***> wrote: Hi, I wonder if it is okay and *more* robust [...] 'More' compared with what? A vs A+B A+C vs A+C+B A+C+D vs A+C+D+B All these three comparisons are equal to just testing for the effect of B (assuming you have a one-hot encoding for your conditions). Best, Constantin — Reply to this email directly, view it on GitHub <#40 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AG6RZ3KLHJOUSELOLQQRPLDWINNE5ANCNFSM6AAAAAASAVRBSU> . You are receiving this because you authored the thread.Message ID: ***@***.***>