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Questions tagged [limma]

limma is a bioconductor package used for linear models in differential expression or methylation analyses

limma is a package for the analysis of expression or methylation data, especially the use of linear models for analysing designed experiments and the assessment of differential expression.

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How do I tell R package Limma what to use as "targets" in read.idat()?

I am analyzing some microarray data. For each donor, I have a "before intervention" and an "after intervention" idat file. I have successfully read these into R using the Limma package with the read.idat() function. However, the resulting object…
EmmaH
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How to reduce dimension of gene expression matrix by calculating correlation coefficients?

I am in interested in finding Pearson correlation coefficients between a list of genes. Basically, I have Affymetrix gene level expression matrix (genes in the rows and sample ID on the columns), and I have annotation data of microarray experiment…
Jerry07
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Design matrix for edge R analysis?

I would like to compare Q method against L method, and I have considered 2 different contrasts (at the end), but I am not sure which on is correct? There are 2 different methods (Q and L) and from each one there are 2 biological replicates (L4,L6-L8…
star
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Statistical testing for each row to create a volcano plot in R?

I currently have a dataset in R where for each gene, I have the log2 expression for four daphnia exposed to copper (columns 2:5), and four control daphnia (columns 6:9). The head of the data frame is shown below: GENE_ID s_MC13_A9_Cu…
A.Carter
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Error message specific to limma employed using R 2.15.2

I recently updated R, and code I had written using the limma package before now returns an error. The code was classes = c(rep('Phenotype1',), rep('Phenotype 2',)) classes=…
Ankur Chakravarthy
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smallRNA-seq analysis batch correction in limma

Good morning, I am currently trying to analyse a small-RNA sequencing dataset using limma package and the voomLmFit function. However, I am experiencing some issues with the p-value distribution, with some of the comparisons I am testing showing odd…
Eleonora Manitta
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limma model.matrix design for crossover study

I'm working with data from a crossover disease study to run limma on. The data would look something like this: If I wanted to create a design matrix where I cared about how gene expression changes with condition interacting with time, would it look…
Michael Yoon
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Can't get design matrix for limma to include all levels of factors

I am working with proteomics data using Limma. I am having trouble getting my design matrix to recognize the different levels of my factors. The factors of my metadata are set up as follows: tissue <- factor(field.order$Tissue, levels = c("A", "G",…
Rho Thygesen
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Cyclic loess leading to complete rows of NA

I am currently evaluating normalization methods on proteomics data. As proteomics data are often affected by a high extent of missingness, filtering of proteins with too many missing values is applied (imputation is not wanted). However, some…
Arend Lis
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R limma analysis result error in defined functions

When I use functions to simplify limma analysis: LimmaAnalysis <- function(){contrastMatrix = makeContrasts(RNA2-RNA1, levels = design)} that is supposed to equal to contrast.matrix = makeContrasts(RNA2-RNA1,levels=design) But once I used my own…
user21341003
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Problem getting PlotMAXY to work in R, packages loaded: beadarray and limma

Can someone tell me what is wrong in an as simple as possible way, I'm a complete novice in R. 1 library (beadarray) 2 library (limma) 3 dataFile <- "/Users/neophytoskouphou/Desktop/Bioinformatics/LA_4.txt" 4 BSData <- readBeadSummaryData(dataFile,…
Neophytos Kouphou
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Reorder dendrogram in R

I want to plot a heatmap where the x-axis is clustered by "normal" and "KIRP" from left to right. Currently, my code clusters by dendrogram/similarity, and unfortunately I have one outlier "KIRP" on the left-most. I want to move this "KIRP" sample…
melolilili
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Building model matrix to correct for batch effect with biological and technical replicates

I recently conducted some MASS SPEC for my samples. Each sample was run thrice through the machine. However, there was a large space of time between the first run and the consequent second and third run (both run at the same time), so I would like…
Maria Faleeva
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Limma moderated t test VS stat_compare_means: why do the values differ?

I've done differential expression on a huge list of genes and I'm selecting only the significant ones among an external list of genes that I want to study. When I represent my significant ones on the barplot, the p-values I obtained from the…
Beth
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how to convert MA list to expression matrix?

I am doing differential expression of Agilent two-channel microarray analysis and I got the MA list and I want to convert it to expression matrix, can I use MAlist$A to produce it as it is log2 values. the M matrix has a lot of negative values and…
aSRA
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