Bioconductor Modelmatrix

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limma modelmatrix pairedanalysis Proteomics

written 10 weeks ago by svlachavas ▴ 840

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limma modelmatrix

updated 4 months ago by Gordon Smyth 52k • written 4 months ago by kyj2226 • 0

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ALDEx2 modelmatrix covariates

20 months ago amir • 0

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DESeq2 limma modelmatrix edgeR designmatrix

updated 3.4 years ago by Gordon Smyth 52k • written 3.5 years ago by rebecca.lea.johnston • 0

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interactionterm edgeR modelmatrix

4.2 years ago • updated 4.1 years ago ahsindoomilup • 0

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Comment: DESeq2 estimateSizeFactors with control genes by sofia.rigou • 0

I am also trying to use this function to estimate sizefactor based on RT-dPCR data but estimateSizeFactor only takes integers. Should I mul…

Comment: DiffBind custom normalization factor by Abbie • 0

Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…

Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k

All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…

Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0

Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…

Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k

For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…

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clusterProfiler-GO enrichment Error

A: Machine learning in R book

Data preparation and Machine learning on time course RNAseq data

Answer: Use of org.Rn.eg.db with GRCr8 reference genome

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