How to extract P-Values and LogFC from lrTest in MAST?

Hi all,

after running lmTest <- lrTest(zlmCond, Hypothesis('grouplate')) in the MAST package, how do i get the pvalues and logfoldchanges?

I would very much appreciate any help!

mast lrtest pvalue logfc

• 686 views • link

written 3.3 years ago by Tadeoye •

0 answers

No answers yet.

More posts like this

how to run ROSE to find super enhnacers-
written 3.0 years ago by Chava •

Hello, I'm pretty new to bioinformatics, and I'm having troubles when trying to run the ROSE package to find SEs. On the website, it's not …
Differential (pathways) expression testing using linear model packages in R (Limma & GSVA)
written 3.4 years ago by Tadeoye •

I'm a novice in this field, and I would be glad if anyone could provide some guidance on analysis of differential expression testing using linear …
Question about aggregating p values from different DE analysis methods for the same RNA-seq dataset
written 3.4 years ago by mmitra •

Hi all, I have an RNA-seq dataset (comparing two different conditions) that I have analyzed using four different methods of differential expression (DE) analysis: DESeq2, …
How to change SNP annotation in minfi function dropLociWithSnps (EPIC methylation array data)?
written 3.5 years ago by Satu •

Hi, I would like to filter out probes with SNPs at CpG site or SBE site, and I have used the *dropLociWithSnps* from minfi package …
How to get number of characters (nucleotides) in fasta file
written 5.1 years ago by er.doug.ragnar •

Hi, I have a bunch of fasta files from refseq and I want to know how many bases are on each one. I want to …
Testing Distances in Phylogenetic Trees
written 7.1 years ago by ResearchR

Dear all, I am running a phylogenetic analysis (R-package 'ape') based on methylation data. The samples in my phylogenetic tree can be grouped in three …
Separating text from one column in R
written 7.1 years ago by e.jabbari •

Hi! I appreciate this is a very basic question but I'm new to the R game so any help offered would be very much appreciated. …
Differential expression with MAST using scran-normalized data
written 7.9 years ago by smt8n •

Hi, I am trying to get DE genes from a scRNA-seq using MAST. The data I am supplying were normalized using scran package. In the …
outside mothur: remove pre-clusters associated with negative control from all groups: bash commands?
written 9.7 years ago by careymsuehs •

Hi. I've been using the miseq mothur pipeline. After pre-clustering I would like to remove negative-control-associated preclusters from all groups/samples. I'm looking for any help …
Arlequin Input Format
written 12.5 years ago by Carl •

<p>Hi everyone,</p> <p>I am having problems with Arlequin, since its guide it's not very clear.. How do I create a proper input file? I have …