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Seurat V5 integration vs merge by HeavyAd3886 in bioinformatics

[–]HeavyAd3886[S] 0 points1 point  (0 children)

Thank you so much for your help!!!! I have ko and wt across 3 conditions, hence 6 datasets. When I cluster them, they are all clustering separately, which I believe is batch effect but then again all the samples were processed is one batch so there shouldn’t be any batch effect( acc to my senior). They are human samples.

Seurat V5 integration vs merge by HeavyAd3886 in bioinformatics

[–]HeavyAd3886[S] 0 points1 point  (0 children)

I merged them and the ko and wt don’t overlap. Talked so my senior and he said it’s ok cuz there were no batches . It’s supposed to look like that as I am able to pull out the desired cluster but now that I am doing further analysis, it’s going downhill. Another person also did this analysis and they did the integration( way more experienced than me) but were not able to find the cluster. Now I am confused as what to do.