Showing : EdgeR • reset
0
votes
2
replies
861
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I need help with EdgeR!
edgeR
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
0
votes
2
replies
1.4k
views
Analyzing barcode sequencing experiments with DESeq2/edgeR
edgeR DESeq2
updated 2.8 years ago by • 0 • written 3.3 years ago by • 0
0
votes
2
replies
1.2k
views
TnSeq as ZINB? Alternatives in R?
DESeq2 R edgeR Python TnSeq
updated 2.8 years ago by • 0 • written 2.9 years ago by ▴ 90
0
votes
0
replies
740
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
2.8 years ago Bogdan ▴ 670
3
votes
6
replies
1.8k
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
2.8 years ago mohammedtoufiq91 ▴ 10
4
votes
6
replies
1.7k
views
Question on creating right design matrix in edgeR
R designmatrix edgeR limma model.matrix
2.8 years ago Abdul ▴ 20
5
votes
6
replies
3.2k
views
How to interpret Histogram of average log2 CPM filtering in EdgeR?
CPM filterByExpr edgeR histogram rowsums
2.8 years ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
1.2k
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
2.9 years ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
2.2k
views
Getting this error while trying to use edgeR "Error in as.vector(x, mode) : cannot coerce type 'closure' to vector of type 'any'"
edgeR edge
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
0
votes
1
reply
1.5k
views
unable to load edgeR after installing it
edgeR
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
2
votes
4
replies
5.7k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
2.9 years ago mohammedtoufiq91 ▴ 10
1
vote
12
replies
3.6k
views
normalization of ChIP-seq data by using the spike-ins or by using total library sizes
DESeq2 edgeR limma
updated 2.9 years ago by 43k • written 2.9 years ago by ▴ 670
1
vote
3
replies
1.8k
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
3
votes
6
replies
2.1k
views
One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 2.9 years ago by • 0
2
votes
5
replies
1.6k
views
Can we massively improve RNA-Seq results by slightly reducing the counts in it?
edgeR RNAseq123
updated 2.9 years ago by 53k • written 2.9 years ago by ▴ 50
1
vote
2
replies
1.4k
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
2.9 years ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
1.5k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
3
votes
6
replies
3.4k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
2.9 years ago Sara • 0
0
votes
4
replies
1.6k
views
paired tests with tidybulk and edgeR
edgeR R tidyverse tidybulk
2.9 years ago Amit Indap ▴ 10
3
votes
7
replies
2.8k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 2.9 years ago by 53k • written 3.0 years ago by • 0
2
votes
1
reply
1.0k
views
Different sequencing depth between replicates and samples
DESeq2 edgeR DiffBind
updated 3.0 years ago by 53k • written 3.0 years ago by ▴ 10
1
vote
4
replies
1.4k
views
RNA-seq analysis between a wildtype vs a double microRNA kockout mouse brain
microRNA gene RNASeqRData edgeR geneontology
3.0 years ago faiza • 0
2
votes
4
replies
1.6k
views
DiffBind and peak counts as input
DESeq2 edgeR DiffBind
updated 2.9 years ago by ★ 5.2k • written 3.0 years ago by ▴ 670
1
vote
7
replies
1.6k
views
statistics : edger or DESeq2 to asses the differential binding using the average scores
DESeq2 edgeR
updated 2.8 years ago by • 0 • written 3.0 years ago by ▴ 670
1
vote
1
reply
3.3k
views
installation of BioC packages on Mac M1 Monterrey OS
limma Bioconductor edgeR
3.0 years ago Bogdan ▴ 670
0
votes
1
reply
2.4k
views
bigwig to counts
DESeq2 edgeR bigwig limma
3.0 years ago • updated 2.7 years ago Bogdan ▴ 670
1
vote
4
replies
1.8k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM edgeR qsea MEDIPS
updated 3.1 years ago by • 0 • written 3.1 years ago by ▴ 20
0
votes
11
replies
5.4k
views
edgeR contrasts
edgeR
updated 2.2 years ago by 68k • written 3.1 years ago by • 0
3
votes
6
replies
2.1k
views
variance decomposition formula
edgeR
3.1 years ago Xinwei • 0
-6
votes
4
replies
1.2k
views
is it possible and reasonable for edgeR to derive DEGs from a complicated contrast or contrast of contrast?
complicated.contrast edgeR DEGs
3.1 years ago Mike • -60
1
vote
1
reply
869
views
How to interpret FC and pesudocounts in EDGER using glmLRT?
edgeR
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
0
votes
0
replies
795
views
Argument is of length zero in variancePartition/Dream
expression variancePartition edgeR
3.2 years ago Jonathan • 0
1
vote
4
replies
9.3k
views
TPM normalization starting with read counts
edgeR DESeq2
updated 3.1 years ago by 53k • written 3.2 years ago by • 0
3
votes
4
replies
1.4k
views
edgeR processAmplicons not recognizing hairpin sequences
edgeR
updated 3.2 years ago by 53k • written 3.2 years ago by ▴ 10
1
vote
1
reply
1.3k
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq Normalization TMM edgeR
updated 3.2 years ago by 53k • written 3.2 years ago by ▴ 10
3
votes
4
replies
3.5k
views
Why Negative value from GSVA
GSVA RNASeq edgeR
3.3 years ago Yang Shi ▴ 10
5
votes
8
replies
27k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 14 months ago by ▴ 60 • written 3.3 years ago by ▴ 30
1
vote
3
replies
3.0k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
votes
4
replies
3.5k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
3.3 years ago Mohamed ▴ 30
1
vote
8
replies
2.3k
views
edgeR design matrix with multiple cell types and combination treatments
DifferentialExpression celltype treatment edgeR limma
3.3 years ago giBio • 0
0
votes
1
reply
1.7k
views
dispersion in edgeR
Sequencing edgeR Sequencing edgeR
updated 3.3 years ago by 53k • written 15.3 years ago by ★ 6.0k
0
votes
2
replies
1.4k
views
Locating nearest genes in RRBS analysis
hiAnnotator bsseq DifferentialMethylation edgeR RRBSdata
3.4 years ago Mageiros • 0
3
votes
2
replies
1.5k
views
time-series analysis using EdgeR
timecourse edgeR
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
2
votes
3
replies
2.9k
views
Confused about the design matrix in edgeR: How to tell R to consider one level as a reference and the other is a treatment to be compared to that ref.
R edgeR
updated 3.4 years ago by 53k • written 3.4 years ago by ▴ 30
2
votes
2
replies
1.4k
views
Help with constructing design matrix for edgeR/limma
limma design.matrix model.matrix edgeR
3.4 years ago adrianna_07 • 0
2
votes
2
replies
1.4k
views
edgeR : results from goana and kegga functions show opposite sig. p-value
edgeR
3.4 years ago sharvari gujja ▴ 40
5
votes
6
replies
2.8k
views
LogFC values in edgeR - w/wo intercept
design.matrix logFC intercept edgeR model.matrix
3.4 years ago JK Kim ▴ 30
3
votes
3
replies
2.4k
views
Question on RNA-Seq single sample data analysis in EdgeR
R edgeR limma RNASeq Normalization
updated 3.4 years ago by 53k • written 3.4 years ago by ▴ 10
6
votes
5
replies
12k
views
how to understand cpm=1 and how filterByExpr works?
edger
updated 3.4 years ago by ▴ 10 • written 5.1 years ago by ▴ 20
1
vote
1
reply
2.0k
views
after calcNormFactors with EdgeR, how to get TMM normalized matrix?
Normalization edgeR
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
2,031 results • Page 5 of 41
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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