Bioconductor Pre-filtering

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deseq2 pre-filtering

updated 6.5 years ago by Michael Love 42k • written 6.5 years ago by bekah ▴ 40

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2.1k

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microarray affymetrix microarrays pre-filtering filtering nonspecific filtering

updated 7.4 years ago by Wolfgang Huber ★ 13k • written 7.4 years ago by n.lu • 0

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7.2k

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deseq2 pre-filtering

updated 7.7 years ago by Michael Love 42k • written 7.7 years ago by Zach Roe ▴ 10

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1.6k

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DEXSeq rownames pre-filtering

updated 8.8 years ago by Wolfgang Huber ★ 13k • written 8.8 years ago by arom2 • 0

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2.8k

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deseq2 differential expression independent filtering pre-filtering design matrix

9.5 years ago Assa Yeroslaviz ★ 1.5k

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2.0k

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deseq2 pre-filtering

updated 9.6 years ago by Michael Love 42k • written 9.6 years ago by Johannes Rainer ★ 2.1k

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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][…

Votes

A: Up/Down Regulated GeneList from edgeR and R

A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis

Answer: Combining RNAseq and microarray data using edgeR/limma-voom

Answer: How do I merge a list of GRanges?

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Teacher to Gordon Smyth 51k

Popular Question to Guido Hooiveld ★ 4.1k