Questions tagged [limma]

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limma linear model with interaction

I want to run some epigenome wide association studies based on city and pollutant type, could you please suggest if I can get DNA methylation sites (CpG) association based on pollutant type for each ...
bioinfonext's user avatar
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0 answers
28 views

Calculating p-value and adjusted p-value for pre-normalized microarray data with fold change precalculated

I have a microarray dataset with two mutants dataset that has already been normalised, and the fold change values for each gene in each mutant versus the wild type have been calculated. I'm interested ...
shaimaa Hassan's user avatar
1 vote
0 answers
85 views

Q-Q plots and the genomic inflation factor (k)

I have done the limma association analysis using below model design but not sure how to evaluate Potential systematic biases using Q-Q plots and the genomic inflation factor (k). Could you please ...
bioinfonext's user avatar
0 votes
1 answer
51 views

Pathway Enrichment Analysis for one specific pathway?

I have a gene set containing a set of 1500 genes in which I did differential gene expression using limma voom pipeline. After this step I wanted to analyze a specific set of pathways the metabolism ...
Manuel Srgio Sokolov Ravasquei's user avatar
1 vote
1 answer
115 views

How do I correctly format my limma/eBayes code?

Here is part of my data table, which I will call "df": ...
Feynman's user avatar
  • 71
1 vote
1 answer
39 views

How do I fix this limma line?

I'm trying to conduct lmFit on my fread::table matrix: ...
Feynman's user avatar
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1 vote
1 answer
87 views

To find genes that don't change in RNA-seq, Deseq2 has altHypothesis="lessAbs". Is there a way to make limma do the same thing for proteomics?

I love that Deseq2 has altHypothesis="lessAbs" !!!!!!! I've used it a ton for RNA-seq. However, now I'm working with mass spect data using limma. Is there a way to make limma do the same ...
Mary Allen's user avatar
2 votes
0 answers
39 views

Does the contrast matrix I have made address the question I am trying to answer?

I have the following design matrix: mm_noreps.interactions <- model.matrix(~condition*TRAPed) Both variables are factors condition has 4 levels and TRAPed has 2 ...
Angus Campbell's user avatar
1 vote
0 answers
46 views

How to tune and use the MetaVolcanoR package

I conducted a differential expression analysis over several datasets, using LIMMA, each one on its own. For each dataset, I have a data frame of all the genes, with ...
Programming Noob's user avatar
2 votes
1 answer
171 views

Problems in conducting batch effect correction

I am now trying to conduct batch effect correction for my data matrix, whose samples (human) have different gender and come from different sequencing platforms. I have tried ...
Ke Xu's user avatar
  • 21
2 votes
1 answer
61 views

How to use the contrast function in ebayes for making different comparisons

The design matrix i have is this I would like to know how to use they way its done in deseq2 where we can use the contrast function to make particular comparison The code im running to make ...
kcm's user avatar
  • 1,804
2 votes
1 answer
524 views

What is the difference between Normalized Expression in EdgeR vs DESeq2?

I am trying to access the normalized expression in both edgeR and DESeq2, yet the results are different. Does anyone know why? How to get normalized expression using edgeR: ...
Nova's user avatar
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2 votes
1 answer
425 views

Generating contrast matrix for limma in loop

I am trying to generate contrast matrix for different conditions using for loop. ...
user98059's user avatar
  • 347
3 votes
1 answer
186 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 ...
Lukas's user avatar
  • 33
-1 votes
1 answer
191 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? ...
Sam's user avatar
  • 149
0 votes
1 answer
393 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 ...
An Ignorant Wanderer's user avatar
3 votes
1 answer
3k 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 ...
Gian Arauz's user avatar
1 vote
1 answer
143 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 ...
FJ_nw's user avatar
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1 vote
1 answer
194 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 ...
Angus Campbell's user avatar
0 votes
2 answers
221 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 ...
ry0-H's user avatar
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0 votes
1 answer
72 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- ...
Vishal Kumar Sahu's user avatar
0 votes
0 answers
523 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 ...
Gwénolé's user avatar
0 votes
1 answer
2k 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, ...
Sam's user avatar
  • 149
0 votes
1 answer
85 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 ...
Reza Rezaei's user avatar
3 votes
1 answer
2k 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 ...
Reza Rezaei's user avatar
1 vote
0 answers
213 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 ...
Reza Rezaei's user avatar
1 vote
2 answers
41 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 ...
pogibas's user avatar
  • 203
1 vote
0 answers
341 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) ...
Kent's user avatar
  • 105
1 vote
0 answers
51 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 ...
Mr.M's user avatar
  • 21
1 vote
1 answer
183 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 ...
Mr.M's user avatar
  • 21
2 votes
2 answers
2k 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 ...
Kent's user avatar
  • 105
0 votes
1 answer
54 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 ...
Vinay Bharadhwaj's user avatar
0 votes
1 answer
255 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 ...
Lyd's user avatar
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0 votes
1 answer
113 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 ...
Kent's user avatar
  • 105
2 votes
1 answer
127 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 ...
Jerry07's user avatar
  • 145
1 vote
2 answers
64 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 ...
Jerry07's user avatar
  • 145
1 vote
0 answers
142 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: ...
user2300940's user avatar
2 votes
0 answers
60 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 ...
Marcus Emilsson's user avatar
1 vote
1 answer
219 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 ...
holly's user avatar
  • 47
2 votes
1 answer
335 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 ...
L R Joshi's user avatar
  • 719
2 votes
1 answer
148 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 ...
h3ab74's user avatar
  • 836
3 votes
0 answers
266 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: ...
Hayley Sowards's user avatar
2 votes
0 answers
524 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 ...
WCMC's user avatar
  • 121
5 votes
2 answers
655 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 ...
gc5's user avatar
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