Bioconductor Nested design

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deseq2 nested design

updated 5.6 years ago by Michael Love 41k • written 5.6 years ago by katarina.truve • 0

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2.2k

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deseq2 nested design

updated 5.7 years ago by Michael Love 41k • written 5.7 years ago by xie186 • 0

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1.1k

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nested design post hoc edgeR

updated 5.9 years ago by Aaron Lun ★ 28k • written 5.9 years ago by ashley.lu • 0

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1.2k

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edgeR nested design differential expression

updated 6.0 years ago by Gordon Smyth 50k • written 6.0 years ago by chiayi • 0

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1.3k

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edgeR model.matrix nested design reference group

updated 6.0 years ago by Aaron Lun ★ 28k • written 6.0 years ago by ri.lars ▴ 40

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969

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deseq2 multiple factor design nested design

6.3 years ago • updated 6.2 years ago michael.steffen ▴ 20

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4.5k

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deseq2 multiple factor design nested design interaction term

updated 7.0 years ago by Michael Love 41k • written 7.0 years ago by zahra.aboukhalil • 0

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1.7k

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deseq2 interaction model nested design

7.1 years ago glocke01 ▴ 10

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1.4k

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edgeR removeBatchEffect nested design

updated 7.5 years ago by Aaron Lun ★ 28k • written 7.6 years ago by Jenny Drnevich ★ 2.0k

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1.5k

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multifactor nested design deseq2

7.6 years ago swaegers.janne • 0

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1.5k

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edger multifactor nested design

7.7 years ago • updated 7.6 years ago swaegers.janne • 0

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1.0k

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limma edger nested design

updated 7.6 years ago by Ryan C. Thompson ★ 7.9k • written 7.6 years ago by xluong • 0

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2.5k

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edger differential gene expression without replicate nested design help

updated 7.8 years ago by Aaron Lun ★ 28k • written 7.8 years ago by knipehf • 0

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edger nested design rnaseq

updated 8.9 years ago by Ryan C. Thompson ★ 7.9k • written 8.9 years ago by mrwarner09 • 0

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2.3k

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deseq2 Nested design random variable

updated 8.9 years ago by Michael Love 41k • written 8.9 years ago by Silva • 0

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Comment: Help with error using camera() in limma by Chris • 0

Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.

Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0

Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.

Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0

Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks

Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k

The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …

Comment: Help with error using camera() in limma by James W. MacDonald 65k

Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …

Votes

C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB

C: Extremely big genes in annotation TxDb packages

Make custom Txdb class objects from Txdb

Comment: Help with error using camera() in limma

Answer: Help with error using camera() in limma

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