Showing : TMM • reset
5
votes
2
replies
689
views
PhD student
TMM limma
10 months ago Nisha • 0
1
vote
1
reply
771
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 15 months ago by 50k • written 15 months ago by • 0
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
839
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq Normalization TMM edgeR
updated 21 months ago by 50k • written 21 months ago by ▴ 10
7
votes
12
replies
4.8k
views
.fastq to .txt conversion for EdgeR package and merging two paired end sequence files
EdgeR normalization fastq txt TMM
updated 24 months ago by 50k • written 8.5 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 ★ 5.2k • written 2.1 years ago by • 0
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 2.6 years ago by 41k • written 2.6 years ago by • 0
0
votes
2
replies
935
views
How to convert TMM RNA-seq file (generated by edgeR) to list of differentially expressed genes
edgeR DifferentialExpression TMM RNASeq
updated 2.6 years ago by 50k • written 2.6 years ago by • 0
3
votes
2
replies
869
views
Some confuse about the DBA_SCORE_TMM_READS_EFFECTIVE_CPM in DiffBind
diffbind CPM TMM
updated 4.1 years ago by ★ 5.2k • written 4.1 years ago by ▴ 40
3
votes
1
reply
1.6k
views
Correct use of TMM / normalization factors based on large bins
csaw TMM
4.7 years ago ATpoint ★ 4.1k
1
vote
1
reply
881
views
How to normalize RNA-seq when 50% genes are DE? (TMM)
limma TMM differential expression normalization rnaseq
updated 5.1 years ago by 65k • written 5.1 years ago by • 0
1
vote
4
replies
1.7k
views
Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 5.4 years ago by 50k • written 5.4 years ago by ▴ 20
6
votes
7
replies
1.9k
views
Normalization for small non-coding RNA
TMM deseq2 smallrna rnaseq
updated 5.4 years ago by ▴ 510 • written 5.4 years ago by ▴ 80
1
vote
4
replies
2.1k
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
0
votes
1
reply
1.1k
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
3
votes
7
replies
5.8k
views
Limma PlotMDS: what values should be used?
limma edger plotmds tmm masigpro
6.4 years ago dacaba.92 ▴ 10
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
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
7.1 years ago aec ▴ 90
2
votes
7
replies
5.3k
views
Gene Expression Matrix (CPM)
cpm gene expression matrix tmm normailzation
7.2 years ago kkadzi25 • 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 ★ 5.2k • written 7.3 years ago by • 0
5
votes
4
replies
3.2k
views
Normalization factor in TMM method
TMM normalization edgeR
updated 7.6 years ago by 65k • written 7.6 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 ★ 5.2k • written 8.0 years ago by • 0
2
votes
2
replies
1.3k
views
Sample sizes must be equal for TMM?
TMM edgeR
7.9 years ago humberto_munoz • 0
5
votes
6
replies
2.0k
views
Getting normalized read counts from region counts
regionCounts TMM csaw
7.9 years ago saadmurtazakhan ▴ 10
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
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
2
votes
5
replies
11k
views
Normalization of RNA-seq data: between samples and within samples
rnaseq normalization tpm tmm
8.6 years ago nickbern92 • 0
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
28 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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