Bioconductor Replicates

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386

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DESeq2 timecoursedata replicates

updated 6 months ago by Michael Love 40k • written 7 months ago by fepesanz8 • 0

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1.8k

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deseq2 R bioconductor RNA_Seq replicates

updated 3.8 years ago by swbarnes2 ★ 1.3k • written 3.8 years ago by aishu.jp ▴ 30

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1.4k

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rnaseq deseq2 differential expression batch effect replicates

updated 4.0 years ago by Michael Love 40k • written 4.0 years ago by Nik dAK ▴ 10

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3.0k

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deseq2 replicates error DESeqDataSetFromMatrix

updated 4.5 years ago by Michael Love 40k • written 4.5 years ago by Yonatan Amzaleg • 0

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2.4k

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limma proteomics replicates

updated 5.2 years ago by Aaron Lun ★ 28k • written 5.2 years ago by ivansilbern • 0

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1.7k

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limma duplicatecorrelation replicates

6.4 years ago rwalke13 • 0

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1.4k

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deseq2 replicates

updated 6.7 years ago by Michael Love 40k • written 6.7 years ago by le2336 ▴ 20

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4.6k

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DESEQ deseq2 deseq replicates biologicalreplicates

7.8 years ago wd ▴ 30

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1.1k

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rnbeads replicates

updated 7.9 years ago by rnbeads • 0 • written 7.9 years ago by Jon Manning ▴ 40

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804

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replicates

8.1 years ago efratdahan21 • 0

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2.1k

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edgeR rna-seq replicates

updated 8.6 years ago by James W. MacDonald 63k • written 8.6 years ago by eb0906 • 0

11 results • Page 1 of 1

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Comment: DESeq2, results(dds, name = <reference>) interpretation results by Rockbar • 0

When I apply the model.matrix approach for getting the contrasts, the code > mod_mat <- model.matrix(design(dds), colData(dds)) > CondA.t…

Comment: DESeq2, results(dds, name = <reference>) interpretation results by Rockbar • 0

Yes, I agree, the correct contrast setting is quite challenging. The vignette says >contrast: a list of 2 character vectors: the names of…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

Advantage and disadvantage depends on the aim, what you plan to do with them (testing, plots, etc.). lengthScaledTPM puts back *in* the ge…

Comment: DESeq2, results(dds, name = <reference>) interpretation results by James W. MacDonald 63k

No, putting -1 in the design matrix is a cell means model, which is the opposite. If you used `~ Cond + Cond:Time`, you would specify a fac…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

Thank you for the response and apologies for my late reply. I think I´m starting getting the concept now. The hints with the cqn is quite …

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Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?

Answer: Remove duplicates of colData in TreeSummarizedExperiment

Awards • All

Scholar to James W. MacDonald 63k