Showing : FireBrowse • reset
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Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2 tximport tcga rsem firebrowse
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
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Difficulty in finding DEG using TCGA data from FireBrowse
TCGA FireBrowse limma DEG
updated 6.6 years ago by ▴ 830 • written 6.6 years ago by ▴ 30
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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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