Showing : tmm • reset
7
votes
12
replies
4.7k
views
.fastq to .txt conversion for EdgeR package and merging two paired end sequence files
EdgeR normalization fastq txt TMM
updated 23 months ago by 50k • written 8.4 years ago by • 0
6
votes
7
replies
1.9k
views
Normalization for small non-coding RNA
TMM deseq2 smallrna rnaseq
updated 5.4 years ago by ▴ 490 • written 5.4 years ago by ▴ 80
6
votes
4
replies
3.2k
views
Can edgeR TMM normalization be used for other count data?
edgeR tmm normalization counts
updated 7.0 years ago by 65k • written 7.0 years ago by ▴ 40
5
votes
2
replies
665
views
PhD student
TMM limma
9 months ago Nisha • 0
5
votes
6
replies
1.9k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
7.9 years ago saadmurtazakhan ▴ 10
5
votes
4
replies
3.2k
views
Normalization factor in TMM method
TMM normalization edgeR
updated 7.5 years ago by 65k • written 7.5 years ago by ▴ 10
4
votes
1
reply
4.7k
views
norm.factors in TMM normalisation
edgr tmm normalization
updated 8.5 years ago by ★ 28k • written 8.5 years ago by ★ 1.5k
4
votes
3
replies
2.8k
views
TMM Manual Calculation to be used in MATLAB on miRNA count data
matlab calcnormfactors TMM edgeR
updated 8.9 years ago by 50k • written 8.9 years ago by • 0
3
votes
2
replies
853
views
Some confuse about the DBA_SCORE_TMM_READS_EFFECTIVE_CPM in DiffBind
diffbind CPM TMM
updated 4.1 years ago by ★ 5.1k • written 4.1 years ago by ▴ 40
3
votes
7
replies
5.7k
views
Limma PlotMDS: what values should be used?
limma edger plotmds tmm masigpro
6.3 years ago dacaba.92 ▴ 10
3
votes
1
reply
1.6k
views
Correct use of TMM / normalization factors based on large bins
csaw TMM
4.6 years ago ATpoint ★ 4.0k
2
votes
1
reply
1.6k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 2.5 years ago by 41k • written 2.5 years ago by • 0
2
votes
5
replies
11k
views
Normalization of RNA-seq data: between samples and within samples
rnaseq normalization tpm tmm
8.5 years ago nickbern92 • 0
2
votes
2
replies
1.3k
views
Sample sizes must be equal for TMM?
TMM edgeR
7.8 years ago humberto_munoz • 0
2
votes
7
replies
5.3k
views
Gene Expression Matrix (CPM)
cpm gene expression matrix tmm normailzation
7.2 years ago kkadzi25 • 0
2
votes
3
replies
2.5k
views
How to deal with up to 75% of DE genes in RNA-seq (TMM, edgeR) ?
differential expression TMM normalization rnaseq edger
7.0 years ago aec ▴ 90
1
vote
4
replies
1.1k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM edgeR qsea MEDIPS
updated 19 months ago by • 0 • written 19 months ago by ▴ 20
1
vote
1
reply
816
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq Normalization TMM edgeR
updated 20 months ago by 50k • written 20 months ago by ▴ 10
1
vote
1
reply
738
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 14 months ago by 50k • written 14 months ago by • 0
1
vote
4
replies
2.0k
views
processing of (salmon) gene counts for eqtl analysis
salmon tximport gene length eqtl TMM
updated 6.0 years ago by 41k • written 6.0 years ago by ▴ 120
1
vote
1
reply
868
views
How to normalize RNA-seq when 50% genes are DE? (TMM)
limma TMM differential expression normalization rnaseq
updated 5.0 years ago by 65k • written 5.0 years ago by • 0
1
vote
2
replies
1.2k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.1 years ago by ★ 5.1k • written 2.1 years ago by • 0
1
vote
4
replies
1.7k
views
Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 5.3 years ago by 50k • written 5.3 years ago by ▴ 20
1
vote
18
replies
3.2k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 10
0
votes
1
reply
1.9k
views
DiffBind TMM normalization
Rory Stark diffbind TMM edgeR chipseq
updated 7.8 years ago by ★ 5.1k • written 8.0 years ago by • 0
0
votes
1
reply
1.0k
views
Limit on significant genes for TMM normalization
normalization quantile normalization tmm edger
updated 6.2 years ago by 50k • written 6.2 years ago by • 0
0
votes
3
replies
1.9k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind chip-seq normalization deseq2 tmm
updated 7.3 years ago by ★ 5.1k • written 7.3 years ago by • 0
0
votes
2
replies
925
views
How to convert TMM RNA-seq file (generated by edgeR) to list of differentially expressed genes
edgeR DifferentialExpression TMM RNASeq
updated 2.5 years ago by 50k • written 2.5 years ago by • 0
28 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq filtering specific to contrasts by Michael Love 41k
Right, I was suggesting subsetting as a valid choice for "treatment and control samples at each timepoint"
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Fair enough, I guess it depends on the comparison being made, right? If one was interested in a feature comparing Timepoint A vs B, then it…
Comment: DESeq2 setting significant p-value by Dev • 0
Sir but when I put in the expression data via the csv file, it was showing the gene names then but now when i set it in the form factor it …
Answer: OrgDb for maize by James W. MacDonald 65k
``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…
Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0
Understood, Thank you very much for the reply, very kind.
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Awards • All
Popular Question to shepherl 3.8k
Popular Question to BioinfGuru ▴ 30
Popular Question to Gordon Smyth 50k
Scholar to Peter Hickey ▴ 740
Popular Question to sropri • 0
Locations • All
United States, 1 minute ago
Ireland, 2 minutes ago
UPF, Barcelona, Spain, 2 minutes ago
United States, 2 minutes ago
Netherlands, 9 minutes ago
Traffic: 897 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6