Questions tagged [limma]

The tag has no usage guidance.

11 questions with no upvoted or accepted answers
Filter by
Sorted by
Tagged with
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
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
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
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 ...