Bioconductor Replicates

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3.3k

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deseq2 R bioconductor RNA_Seq replicates

updated 5.5 years ago by swbarnes2 ★ 1.4k • written 5.5 years ago by aishu.jp ▴ 30

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1.5k

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rnbeads replicates

updated 9.5 years ago by rnbeads • 0 • written 9.5 years ago by Jon Manning ▴ 40

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5.7k

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DESEQ deseq2 deseq replicates biologicalreplicates

9.5 years ago wd ▴ 30

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1.9k

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deseq2 replicates

updated 8.3 years ago by Michael Love 43k • written 8.3 years ago by le2336 ▴ 20

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3.0k

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limma duplicatecorrelation replicates

8.0 years ago rwalke13 • 0

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3.7k

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limma proteomics replicates

updated 6.8 years ago by Aaron Lun ★ 28k • written 6.8 years ago by ivansilbern • 0

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3.7k

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deseq2 replicates error DESeqDataSetFromMatrix

updated 6.1 years ago by Michael Love 43k • written 6.1 years ago by Yonatan Amzaleg • 0

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2.5k

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rnaseq deseq2 differential expression batch effect replicates

updated 5.7 years ago by Michael Love 43k • written 5.7 years ago by Nik dAK ▴ 10

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950

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DESeq2 timecoursedata replicates

updated 2.2 years ago by Michael Love 43k • written 2.2 years ago by fepesanz8 • 0

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2.6k

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edgeR rna-seq replicates

updated 10.3 years ago by James W. MacDonald 68k • written 10.3 years ago by eb0906 • 0

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2.1k

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conditions replicates SmallRNAData DESeq2

updated 16 months ago by Kevin Blighe ★ 4.0k • written 17 months ago by samer ▴ 10

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1.0k

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replicates

9.7 years ago efratdahan21 • 0

12 results • Page 1 of 1

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Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k

Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…

Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0

Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…

Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0

The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …

Comment: parameters of filterByExpr by Paul Harrison ▴ 110

It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…

Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k

voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…

Votes

Comment: Check removeBatchEffect effectiveness

Answer: Check removeBatchEffect effectiveness

A: what should I do with many zero counts from Salmon quantification

Comment: parameters of filterByExpr

GAlignments Cigar to GRanges

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