Questions tagged [limma]

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5
votes
2answers
257 views

Smallest group size for differential expression in limma (bulk RNA-Seq)

I am reading Smyth et al. (ref. 1). I want to run differential expression analysis on a bulk RNA-Seq dataset in which each group is composed by 2 samples. In the paper previously cited it is written ...
4
votes
1answer
156 views

R limma alternatives in Python

The R package limma is ideal to perform differential expression analysis. Is there any limma alternative in Python? I'm trying ...
3
votes
1answer
711 views

Removing Batch Effect in Heatmaps after Differential Gene Expression Analysis

I'm working on a dataset in which the first replicate of each group is one batch and the second replicate is in a second batch. After checking the PCA plot and ...
3
votes
0answers
204 views

Differentially methylated position analysis in a related sample?

I'm trying to figure out how to do a DMP analysis (using minfi dmpFinder) on a related sample (if it's even possible). Right now the code (not written by me) is: ...
2
votes
2answers
1k views

TPM or rlog(CPM) for comparing expression?

I want to see the expression of a gene in a group of patient amongst the entire cohort using my RNA-Seq data. While I can do a differential expression analysis with limma or DESeq2, I want to see how ...
2
votes
1answer
46 views

Toptable error, wont recognize condition

I am getting a rather strange error from topTable. When I run my code I get Error in fit$coefficients[, coef] : subscript out of bounds from topTable as if it is ...
2
votes
1answer
139 views

How to get log2 fold change of RNA-Seq data for time series experiment?

I know if there is one control and one treatment group it is pretty straight forward to interpret log 2 fold change. But, I have time course experiment. I have infected cells with viruses and I ...
2
votes
1answer
127 views

Significant gene set testing - limma

While I have used my title, it is more of a general statistics question regarding how these significance tests are carried out, these include decideTests and ...
2
votes
0answers
82 views

vst() from DESeq2 vs voom() from limma

I have used both to transform my leukaemia RNA-Seq data for subsequent hierarchical clustering. The result is quite different. Some subtypes of leukaemia only form a cluster (or at least sit closer) ...
2
votes
0answers
52 views

How can `limma` be used to determine genes predictive of a given phenotype?

Using limma within Bioconductor here, which is a linear model package for microarray data and lmFit on gene expression data, I ...
2
votes
0answers
372 views

Different results between paired t-test, paired t-test-like (empirical Bayesian), and mixed effect model

I am learning the R package limma using its user guide. I need help on understanding the difference between the paired t-test, paired t-test-like (empirical Bayesian) and the mixed effect model in the ...
1
vote
2answers
35 views

Identify differentially covered genes only between two samples

I have a question about finding differentially covered regions (coverage represents methylation level which goes from 0 to several thousands). I'm using enrichment based method which can be summarized ...
1
vote
1answer
71 views

Can I use a regular liner regression model when I'm working with DNA methylation data?

I'm new on working with genetics data and I'm just wondering if I can use the lm function when I'm building my models or do I have to use ...
1
vote
2answers
52 views

Any way to quantify the variation of genes that expressed in Affymetrix expression data?

am experimenting preprocessed Affymetrix microarrays expression data matrix (Affymetrix probe-sets in rows (32830 probesets), and RNA samples in columns (735 samples)) for my downstream analysis. Here ...
1
vote
1answer
20 views

Help with Limma-model

I'm starting to use Limma to find differential expressed sites within my data and would like to ask if my approach was correct. The data has a control and a treatment set, each containing data of 48 ...
1
vote
1answer
132 views

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 ...
1
vote
1answer
25 views

Help with DIA-Mass Spectrometry data analysis with several conditions (limma?)

I am trying to learn how to analyse normalised DIA-MS data and I am struggling with it :// The original dataset I got is (6 conditions (2 samples each)) with 3 technical replicates (total: 36 sample ...
1
vote
0answers
23 views

How can I get the estimate of lmFit function form limma package

This is the first time that I used lmfit function from the limma package I'm a little bit confused on how to interpret the result. is there a way to get the ...
1
vote
0answers
91 views

Gene ratio as imput in limma

I have a data frame with gene-expression ratio. Is it possible to input this into limma/voom to find signinficannt gene-ratios between groups of samples? my data: ...
0
votes
1answer
11 views

How is the t-statistic value calculated in GEO2R or Bioconductor?

I was trying to calculate t-statistics using Python's scipy and numpy as np- ...
0
votes
1answer
370 views

Details of DESeq2 modeling a batch effect

When correcting my data for a batch effect using removeBatchEffect, some of the gene expression values become negative. When searching for differentially expressed genes, I do not use the data above, ...
0
votes
1answer
49 views

the variation between treatments is less than the variation between replicates in RNA-seq data

I have a set of RNA-seq samples from targeting different proteins in a complex with siRNAs. However, the ...
0
votes
1answer
41 views

How to perform DE analysis for each sample

I am new to R and biocondunctor. I have the normalized expression values for 20 samples for a disease and for 10 controls. I wanted to get the differential expressed values for each sample with all 10 ...
0
votes
1answer
169 views

Correlate DEGs from DESeq2, EdgeR and Limma results

I have a lists of DEGs identified by DESeq2, EdgeR and Limma. I would like to correlate the the gene rankings in the lists to decide on a package to use in downstream analysis. I am havig a few ...
0
votes
1answer
82 views

Single sample in group: normal pipeline or Kal's Z test

As stated, which one is better for differential expression analysis? When I say normal pipeline I mean limma-voom, edgeR and DESeq2 pipeline for standard analysis. Kal's z test is mentioned in this ...
0
votes
1answer
32 views

Limma decideTests function: what kind of multiple hypothesis testing correction does parameter "method" involve?

What kind of multiple hypothesis testing correction does method="global" do in Limma's decideTests function? According ...
0
votes
1answer
57 views

Determining what RNAseq data is filtered on volcano plot

I am using RNA seq data to analyze genes via a volcano plot comparing differential gene expression of bacteria with and without antibiotic in R. After having created my plot, I am unsure why some of ...
0
votes
0answers
60 views

Troubles implementing LIMMA for paired samples (before/after treatment) comparaisons

i try to implement LIMMA for paired samples in order to compare gene expression before/after treatment. But...i'm not confident in my results since every single gene expression seems to be ...
0
votes
0answers
105 views

Differential Gene Expression with Replicates for some of the samples

[this question has also been posted on Biostars; some additional clarification from there has been copied into this question] I've been asked to analyse a set of samples in which their control sample ...
0
votes
0answers
62 views

Any way to filter out highly correlated genes with limma linear model?

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 observation where sample ID in the rows and ...
-1
votes
1answer
29 views

Assumptions of batch effect removal

What does removing a batch effect (e.g. with limma::removeBatchEffect) assume about the batch effect? Does it assume simply a constant batch effect for each level? ...