User: townsendae

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townsendae0
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Posts by townsendae

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Can I run cellassign on samples independently if there is batch effect present?
... I am running the R cellassign algorithm on a set of 9 samples. Each sample consists of cells extracted from lungs. When I look at a UMAP plot and color by sample origin, there is a notable batch effect. So, here's my question.. Can I run the cellassign algorithm on each sample independently for cel ...
R batch-effect cellassign rna-seq written 15 days ago by townsendae0
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Comment: C: Should I integrate datasets between conditions if I am doing differential expres
... So you're saying above that the original counts should be used for DE testing and the batch corrected should be used for visualization/clustering. ...
written 21 days ago by townsendae0
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Comment: C: Should I integrate datasets between conditions if I am doing differential expres
... One is a dataset of lung samples from a sample of healthy patients and then the other is lung samples from patients with a condition (completely separate experiments). I believe they both used drop-seq technology. The batch effect was quite pronounced between the different samples in the healthy pat ...
written 21 days ago by townsendae0
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Comment: C: Should I integrate datasets between conditions if I am doing differential expres
... Sorry! Should have specified... it is single cell ...
written 21 days ago by townsendae0
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Should I integrate datasets between conditions if I am doing differential expression analysis between the conditions?
... Hi there, I am new to this website and was hoping someone could answer some questions for me. I have two datasets. One is a control dataset and the other is a dataset where patients have a condition. Both are taken from human lungs, however, they are two entirely separate experiments. I have applied ...

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