Bioconductor Batch-correction

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batch effects limma batch-correction RNAseq RUVseq

updated 4.5 years ago by James W. MacDonald 67k • written 4.5 years ago by bhakti.dwivedi • 0

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batchelor batch-correction mnncorrect fastmnn rna-seq

updated 4.6 years ago by Aaron Lun ★ 28k • written 5.2 years ago by rmf ▴ 20

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sva batch-correction

updated 5.0 years ago by James W. MacDonald 67k • written 5.0 years ago by thkapell ▴ 10

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Comment: Differential Expression Analysis with unbalanced batches without replication bet by Thili • 0

Thank you for your reply. I currently have batch-corrected data processed with scvi-tools (specifically, totalvi) and have followed the sam…

Comment: Problem at champ.load by andrew.gibbons • 0

I'd love to know if anyone has a workaround too. I've tried rolling back ChAMP and R to the previous versions that others have said work wi…

Comment: GOstats kegg analysis in wheat - help - none of the objects in the first column by GV Yoshikawa • 0

Thank you for the reply. I tried swapping columns before asking, it made no difference. head(keggframeData) path_id kegg…

Answer: Differential Expression Analysis with unbalanced batches without replication bet by Gordon Smyth 51k

> Is there an alternative model or approach in tools like edgeR, limma-voom, or DESeq2 or any other that can handle confounded batch effect…

Comment: BiomaRt Possible Ensembl SSL connectivity problems detected. by Adam • 0

I just found this workaround: httr::set_config(config(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE)) at [this Stack Overflow link][…

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A: Up/Down Regulated GeneList from edgeR and R

Answer: How do I merge a list of GRanges?

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