Bioconductor Nested

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407

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DESeq2 multifactorial nested

updated 13 months ago by Basti ▴ 770 • written 13 months ago by jd • 0

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1.0k

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nested DESeq2

updated 2.2 years ago by Michael Love 41k • written 2.3 years ago by yampolsk • 0

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1.0k

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deseq2 Phyloseq Nested

updated 4.1 years ago by Michael Love 41k • written 4.1 years ago by mpuli011 • 0

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746

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deseq2 Paired Nested

updated 4.3 years ago by Michael Love 41k • written 4.3 years ago by julia.chariker ▴ 10

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977

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deseq2 nested de

updated 4.4 years ago by Michael Love 41k • written 4.4 years ago by gaio.transposon • 0

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1.1k

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edgeR nested glm glmQLFit

updated 5.0 years ago by Aaron Lun ★ 28k • written 5.0 years ago by jcalis ▴ 10

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2.5k

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edger nested design matrix differential expression

updated 9.2 years ago by Aaron Lun ★ 28k • written 9.2 years ago by Mauve • 0

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1.8k

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edger nested estimatedispersions

9.2 years ago Mauve • 0

8 results • Page 1 of 1

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Answer: Log-cpm values from limma by Gordon Smyth 50k

The log-cpm values from voom() are not free of batch effect. If you want batch-corrected log-cpm values, we recommend cpm() followed by rem…

Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k

As expected normalization is **way** off, meaning in simple terms that the cloud is too high. The deep-blue area should be along y=0. Try t…

Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0

Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…

Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k

I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …

Comment: Theoretical WGCNA Question by Garrett • 0

Thanks Peter!

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Answer: OrgDb for maize

Comment: significant difference of p-values with dream() after updating VariancePartition

How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output

Comment: DEXSeq DEXSeqDataSet count matrix duplication

Comment: Error in champ.load(): The following specified files do not exist

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