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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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coefficient not estimable model.matrix

I'm making a de analysis using Limma, and I have a lot of samples. I trying to compute the design matrix and then the lmFit(). But when I call lmFit it returns coefficient not estimable refering for the last coefficient in the design matrix.…
Agata
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Error trying to add colours to R ggplot (volcano plot)

Wanted to make a volcano plot that was coloured based on signifcance and differential expression. Made a dataframe using toptable in R from Limma object. Added colour column to to the data frame based on adjusted p value and logfc. So each gene also…
lordjord93
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How to select/exclude specific conditions or cell types for further analysis with Limma?

I'm new to R and Limma, and I tried to analyze a data set using the Limma guide. So far, so good, but now I want to include only 3 of the 5 cell types I have in my data set in "y" and any further analysis. How do I "select" or "exclude"…
astromonocyte
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Limma to Compare Bulk RNA Seq using makeContrasts and eBayes

After a day of googling, I've decided that it'd be better to ask the question here. So the experiment is I have bulk RNA seq data from 3 patients: A, B, C. And their RNA seq data is obtained for pre-treatment, treatment cycle 1, treatment cycle 2,…
DHH
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R Limma P-Value vs Foldchange on cytokine data

I am trying to work with limma from Bioconductor to calculate the p-values and foldchange values and find differentially expressed genes. My data looks like this. 1. CYTO Value ABC1 2.3 ABC2 2.3 ABC3 2.5 ... PQR1 …
Kp_Data
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limma: Error in smooth.spline(lambda, pi0, df = smooth.df) : missing or infinite values in inputs are not allowed

I have one dataset for comparing the control and treatment and use limma for the pval. It worked well with most of my data untile I got one like this. I can tell there are differences between control and treatment. But I got error: " Error in…
L.C
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How to get the underling data of a MA plot?

I would like to use the plotMA function of limma. The example of the documentation works fine: A <- runif(1000,4,16) y <- A + matrix(rnorm(1000*3,sd=0.2),1000,3) status <- rep(c(0,-1,1),c(950,40,10)) y[,1] <- y[,1] + status plotMA(y, array=1,…
Cleb
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Voom transformation of RNA seq raw counts data

I have RNA seq data of raw gene counts that I want to transform for linear modelling. I am trying to voom transform, to do a weighted analysis. Data frame: prac_count_10 gene S1 S2 S3 S4 S5 ENG0000456 0 1 10 145 …
holly
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I get this Error in log2(exprs(eSet)) : non-numeric argument to mathematical function

I work with the gene expression dataset "GSE1824", downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1824. To begin processing this data, I loaded the required packages on R studio: # load libraries library(affy)…
Charles
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paired linear model in R

I am looking for a method to use pairing information in my lm model. My model compares Cancer-Normal for paired samples. value 1.21 2.3 2.2 3.1 1.2 0.12 group "Cancer" "Normal" "Cancer" "Normal" "Cancer" "Normal" pairs 001 001 002 002 003 003 My…
user2300940
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Is it possible to analyse the effect of both factors and numeric variables at the same time in a limma model?

I try to perfom an analysis of gene expression data with the limma r package. My model includes factors and numerical covariates and I'm not able to get the results for both types of variables at once. Here is an example: design <-…
jkd
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Design Matrix using model.matrix function for gene expression

Need some help. My data looks like this: Identifier Sample1 Sample2 Sample3 ...Sample10 Gene1 10.85 9.33 11.04 ... 10.093 Gene2 5.94 7.95 6.46 ... 6.33 ... Gene99 3.93 4.12 7.86 …
Darth Ratus
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How do I get an average for each replicate for each gene?

I am new to R and coding and so this might be a very obvious answer! I have a data set with log2 values for four daphnia replicates for thousands of gene probes, corresponding to various genes (as shown in the image). However, for each replicate I…
A.Carter
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Interpreting linear model formula in limma package

Here is my code for building a design matrix for a linear modelling function: f <- factor(targets$Sample.Name, levels = unique(targets$Sample.Name)) design <- model.matrix(~0 + f) colnames(design) <- levels(f) Am not sure how to interpret the…
Eddy Zavala
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Conducting multiple t-tests without using limma

I am trying to conduct a paired t-test and generate a resulting p-value for some methylation data that I have. The data is in 6 columns: 3 for each patient before treatment and 3 for each patient after treatment. There is one row for each gene…
M Dybala
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