Bioconductor Complex-design

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limma complex-design paired design

updated 7.5 years ago by Aaron Lun ★ 29k • written 7.5 years ago by ML18 ▴ 10

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2.9k

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rnaseqpower sspa sample size sequencing complex-design

updated 9.5 years ago by m.van_iterson ▴ 20 • written 9.5 years ago by roser.navarro • 0

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limma paired samples complex-design

9.7 years ago • updated 9.6 years ago aec ▴ 90

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4.6k

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limma model matrix limma design matrix complex-design

updated 10.2 years ago by Aaron Lun ★ 29k • written 10.2 years ago by Guido Hooiveld ★ 4.1k

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deseq2 multiple factor design complex-design

updated 10.5 years ago by Michael Love 43k • written 10.5 years ago by sifujio • 0

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7.3k

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combat software error rnaseq complex-design

updated 10.9 years ago by Peter Langfelder ★ 3.0k • written 10.9 years ago by Stefano Mangiola ▴ 40

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2.8k

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edgeR complex-design

updated 10.9 years ago by James W. MacDonald 68k • written 10.9 years ago by lwc628 ▴ 20

7 results • Page 1 of 1

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Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200

I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …

Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k

Not sure I understand. You ask how to do something and then show how one would do so.

Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10

Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…

Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200

I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …

Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k

Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…

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How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?

Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea

Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi

Can NanoString data be analyzed using DESeq2?

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