Bioconductor Mixed model

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limma microarray design paired mixed model

updated 6.6 years ago by Aaron Lun ★ 29k • written 6.6 years ago by rasmus.agren • 0

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limma rna-seq mixed model repeated measures

updated 7.0 years ago by Gordon Smyth 52k • written 7.0 years ago by mikhael.manurung ▴ 280

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rna-seq edger mixed model random effects lme4

updated 9.2 years ago by Gordon Smyth 52k • written 9.2 years ago by Ekarl2 ▴ 80

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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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Can NanoString data be analyzed using DESeq2?

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