Tag: MAplot

Log2FC values slightly higher in some genes after DESeq2 shrinkage

Hi, I have a question about DESeq2 LFCshrinkage: Is it possible that some genes have a slightly higher LFC after shrinkage? It happened during my RNAseq DE analysis, I have very deeply sequenced samples with large base means. I tried visualizing using MAplot check, and it looks fine. I’m mainly…

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Deseq2 Multifactor Design – Design Forum

Deseq2 multifactor design – In fact, deseq2 can analyze any possible experimental design that can be expressed with fixed effects terms (multiple factors, designs with interactions, designs with continuous variables, splines, and so on are all possible). We have searched different posts in different forums and i can’t figure out…

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InteractiveComplexHeatmap on DESeq2 object with more than 2 groups

InteractiveComplexHeatmap on DESeq2 object with more than 2 groups 1 Hello all, I’m writing with the hope someone can clarify a doubt I have about the differential heatmap generated by the package InteractiveComplexHeatmap via the simple command interactivate(dds). I read the package documentation at bioconductor.org/packages/release/bioc/html/InteractiveComplexHeatmap.html, but I couldn’t find the…

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Highlight points on a plot

R: Highlight points on a plot maText {marray} R Documentation Highlight points on a plot Description This function may be used to highlight a subset of points on an existing plot, such as a plot produced by plot, maPlot, or maPlot.func. Usage maText(subset=NULL, labels=as.character(1:length(subset)), …) Arguments subset A “logical” or…

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Is there a way to mark up specific genes in MA-plot?

Is there a way to mark up specific genes in MA-plot? 1 Dear, everyone, I have this table, and created MAplot using the following steps. In this plot, I would like to mark up only the genes that I specify:for example, I would like to display the gene name in…

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Tools for Normalizing and Comparing ChIP-seq Samples

data(H3K27Ac, package = “MAnorm2”) attr(H3K27Ac, “metaInfo”) ## Make a comparison between GM12891 and GM12892 cell lines and create an MA ## plot on the comparison results. # Perform MA normalization and construct bioConds to represent the two cell # lines. norm <- normalize(H3K27Ac, 5:6, 10:11) norm <- normalize(norm, 7:8, 12:13)…

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lfcShrink probelm in many 0 count genes RNA-seq data

Hi, Dr love. I post a question about weird MAplot or volcano plot of DESeq2 diff result and also in biostar. ATpoint give a useful answer about too many 0 count genes and prefiltering. It seems that too many 0 count genes makes lfc shrink have a probelm. And I…

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weird MAplot or volcano plot of DESeq2 diff result

Hi, every one. I find a werid MAplot or volcano plot of DESeq reuslt. I am wondering whether you can give me some advice. This diff result is from two cell type bulk RNA-seq. I use two specific marker to get these two cell type using Flow cytometer. I alreadly…

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