Bioconductor Cibersort

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cibersort deconvR immune

updated 16 days ago by ivorychan7777 • 0 • written 15 months ago by 609b0d25 • 0

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normalization r vst cibersort

updated 3.7 years ago by Kevin Blighe ★ 3.9k • written 3.7 years ago by Matan G. ▴ 60

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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…

Comment: PCA plot suggestions by JKim • 0

cross post: https://www.biostars.org/p/9593486/

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k

You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…

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C: null model and DEXSeqDataSet object in DEXSEQ

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Scholar to James W. MacDonald 65k

Supporter to JKim • 0