14 results in 0.0051 seconds.
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Question about using limma for differential analysis
For the Differential analysis I'm using "limma" R package. I'm using RSEM log2 transformed counts data from XENA browser. A matrix "U"... -
RNA Seq analysis
I want to extract differential expressed genes using LIMMA from RNA seq data for three cancer types viz breast, lung and prostate. These data should have... -
Limma selectModel output
I've been given a large RNAseq dataset on a biological process which I know little about. There is a ton of associated sample data, and I've built a... -
Too high adjusted P-values analysing RNA-seq count data with limma
Hello!
I'm trying to analyse an RNA-seq count data matrix with limma. From an input table with about 15000 entries, limma gets 1600 differentially...Last edited by IsBeth; 02-19-2016, 11:13 AM. -
Nested Multi-Level Model for RNA-Seq Differential Expression
I have read several other postings regarding nested models, but they did not seem to exactly capture my particular case, and I'm a bit unsure how to proceed... -
Please HELP! TCGA RNAseq data and Limma
Hi,
Very much a beginner here. I downloaded TCGA RNA seq data, and unzipped the file, and now have a folder of about 80 .txt files with... -
Combining RNA-seq datasets
I searched a lot of threads here and elsewhere without finding anything exactly like this.
I have two RNA-seq datasets from different dates... -
Error in duplicateCorrelation.. limma
Hi,
I am trying to use the duplicateCorrelation function in limma for my data and I get an warning message
Warning messages:... -
FPKMs and Limma R package
Hi!
I have generated a dataset with 9 different biological samples (plus replicates) and have analyzed it using TopHat and CuffLinks. Therefore,... -
model matrix design for multiple siRNAs targeting same gene
Hi,
after lurking here for 2 years or so (and learning so much from this community!) I finally have a question I haven't been able to find an... -
Limma removeBatchEffect question
I'm using limma_3.14.1
Suppose I set up:
data<-c(2,2,3,3,5,6,7,8)
data<-rbind(data,data) # Two row matrix...Last edited by Justin AC Powell; 02-17-2014, 07:26 AM. -
edgeR vs. DESeq vs. baySeq vs. NOIseq vs. SAMseq vs. Limma vs. Cuffdiff 2 vs. EBSeq
A recent paper suggests that cuffdiff 2 is not very sensitive and an overall poor choice for detecting differential expression in RNA-seq studies. Do... -
DESeq on "small genome" data
Hi guys,
I'm interested in your opinion, whether it is a good idea to use DESeq application for DE in an experiment where number of transcripts... -
cuffdiff and limma, puzzled by the differences
Hi all, I've been using cuffdiff for a long time but recently I've given limma (voom) a try for RNA-seq data and compared the results.
The experiment...
