Bioconductor DEP

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DEP

updated 17 hours ago by shepherl 3.8k • written 17 hours ago by Namrata • 0

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limma Differentialenrichmentanalysis DEP

updated 6 weeks ago by Gordon Smyth 50k • written 7 weeks ago by Laura • 0

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LFQ DEPpackage run_app('LFQ') ShinyApps DEP

updated 9 months ago by Ram ▴ 190 • written 10 months ago by d.kozhevnikova ▴ 10

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Proteomics DEP limma

written 2.8 years ago by barrypraveen • 0

4 results • Page 1 of 1

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Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0

Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…

Comment: Finding DEGs by using edgeR by prity6459 • 0

Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …

Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k

It doesn't seem to me that there is necessarily any problem with the analysis. You that there are "too many low-reads" but actually there …

Answer: How to make DGEList and design matrix by edgeR package by Gordon Smyth 50k

Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…

Answer: Finding DEGs by using edgeR by Gordon Smyth 50k

I am not clear what you mean that you have already normalized your data. How exactly did you normalize the data? The best way to do an edg…

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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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