Bioconductor MiRNAseq

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miRNAseq TCGAbiolinks TCGAAnalyze_DEA

3.1 years ago Gandino • 0

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deseq2 miRNASeq designmatrix Batch

updated 4.8 years ago by Michael Love 43k • written 4.8 years ago by anshulmbi • 0

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limma edger voom rnaseq mirnaseq

4.9 years ago atakanekiz ▴ 30

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deseq2 normalization miRNASeq

updated 5.3 years ago by Michael Love 43k • written 5.3 years ago by anshulmbi • 0

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Answer: DESeq2 Heatmap by James W. MacDonald 67k

Two things. First, `scale` is already vectorized, so you don't have to use `apply`. You can instead just do `t(scale(t(mat)))` . Second, th…

Answer: Improve performance of qusage aggregateGeneSet by James W. MacDonald 67k

This support site is meant mostly to help people with questions about using Bioconductor packages rather than posting code improvements. I …

Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k

If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…

Comment: org.Hs.eg.db issue by k.panov • 0

installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(

Comment: MBDseq analysis using qsea package by Lukas ▴ 20

Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…

Votes

C: Limma: how to get same output as topTable but for all the genes ?

A: Processing agilent data by limma

A: Linear regression in DESeq2

Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?

Answer: Issue carrying out DiffBind Analysis at a predefined peak set

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