How to process batches to be able to correct for its effect
Hi everyone,
I'm working on the ALS patients and comparing cases and control of this disorder. I already did single nucleus RNA sequencing for my controls (which were randomized with the samples from different region of case and controls of the same patients and some controls). Now, I would like to do the single cell RNA seq for my controls. But I'm worried that for downstream analysis it could be complicated as for batch correction. I really appreciate if anybody has any experience like this or any recommendation. I have the option to process one of the cases with these samples once more. I was wondering if it worth to do so.
I appreciate any comments
• 1,596 views
•
link
updated
by
rpolicastro
•
written
by
paria •
•
written
by
paria •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
what is the best way to build my design model with DESeq2
written by paria •
-
Why in Heatmap plot my case and control samples of single cell dataset are not well clustered?
written by paria •
-
Why DEG analysis of the same region in two different datasets results in different sets of DEGs?
written by paria •
-
How to convert Seurat object to sce object retaining the HVG
written by paria •
-
What should I do if the gene IDs in my reference dataset and test dataset are different
written by paria •
-
How do I know if I'm overcorrecting my single cell data
written by paria •
-
Does chemistry have significant effects on my single nucleus dataset?
written by paria •
-
Single cell cluster evaluation does not output reasonable number of stable clusters
written by paria •
-
Integration or not?
written by paria •
-
Integration of 10X genomics single-nuclei RNA seq datasets
written by paria •
Out of curiosity why are you performing both snRNA-seq and scRNA-seq on your control samples?
Sorry, I meant sn-RNA sequencing by single cell. I did just sn-RNA seq.
Integration of datasets generally mitigates many of the effects of batch in standard single-cell analysis. See chapters 13 (and additionally 7) in OSCA, or the Seurat integration vignette.