Bioconductor Plotpca

Showing : plotpca • reset

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341

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Rstudio plotPCA DESeq2

5 months ago • updated 4 months ago yee • 0

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612

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plotMA ggplot2 plotPCA DESeq2

updated 6 months ago by Michael Love 41k • written 6 months ago by sara.jacobson • 0

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plotPCA PCA

updated 12 months ago by hediatnani • 0 • written 13 months ago by Yijing • 0

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DESeq2 plotPCA

2.2 years ago • updated 2.1 years ago synat.keam • 0

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plotpca DESeq2

2.3 years ago bjen731 ▴ 10

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plotPCA DESeq2 RUVSeq removebatcheffect()

3.0 years ago elizabethe819 • 0

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DESeq2 RNASeq plotpca

updated 3.2 years ago by Michael Love 41k • written 3.2 years ago by s1760083 • 0

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deseq2 biplot plotpca

updated 4.3 years ago by Michael Love 41k • written 4.3 years ago by ecg1g15 ▴ 20

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638

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deseq2 PlotPCA draw.triple.venn

updated 5.6 years ago by Michael Love 41k • written 5.6 years ago by N. Perera • 0

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602

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deseq2 plotpca

updated 5.6 years ago by Michael Love 41k • written 5.6 years ago by snp31 • 0

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deseq2 plotpca PCa

updated 6.5 years ago by Michael Love 41k • written 6.5 years ago by lirongrossmann ▴ 80

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deseq2 rlog variancestabilizingtransformation plotpca pca

6.6 years ago lirongrossmann ▴ 80

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DESeq2 plotPCA rlog transformation vsd

6.8 years ago Jane Merlevede ▴ 90

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41k

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plotPCA deseq2 labels

updated 7.3 years ago by Federico Marini ▴ 150 • written 7.3 years ago by al-ash ▴ 50

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pca plotpca

7.5 years ago marianarochadesouza • 0

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deseq2 plotPCA PCA rna-seq

7.9 years ago newsomew13 • 0

16 results • Page 1 of 1

Recent ...

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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…

Votes

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0