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Showing :
normalization
•
reset
6
votes
11
replies
4.1k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 10 weeks ago by
Priya
• 0 • written 3.2 years ago by
Marina
▴ 40
5
votes
11
replies
3.2k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 12 months ago by
Sabiha
▴ 20
4
votes
4
replies
2.1k
views
Unlog transformed data in DESeq2
RNASeq
DESeq2
vst
rlog
Normalization
updated 5 months ago by
Gordon Smyth
50k • written 2.4 years ago by
mohammedtoufiq91
▴ 10
2
votes
5
replies
11k
views
Conversion from counts to FPKM
counts
fpkm
fpkm()
normalization
deseq2
updated 7 months ago by
Hamza
• 0 • written 5.5 years ago by
chiara.facciotto
• 0
2
votes
2
replies
748
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2
medianofratiostransformation
StatisticalMethod
Normalization
dispersion
4 months ago
Linton
• 0
2
votes
3
replies
402
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 3 months ago by
James W. MacDonald
66k • written 3 months ago by
Shaimaa Gamal
• 0
2
votes
4
replies
670
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
4 months ago
Sabiha
▴ 20
2
votes
1
reply
327
views
Normalization factors when there is a possible unidirectional expression
limma
Normalization
DifferentialExpression
updated 3 months ago by
ATpoint
★ 4.2k • written 3 months ago by
Shaimaa Gamal
• 0
2
votes
2
replies
453
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
3 months ago
jackafiore
• 0
2
votes
2
replies
432
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
6 weeks ago
Henry
▴ 10
1
vote
6
replies
1.8k
views
can negative value microarray matrix data analysed by limma directly
limma
microarray
normalization
updated 9 months ago by
Gordon Smyth
50k • written 3.7 years ago by
linouhao
▴ 20
1
vote
4
replies
329
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
9 weeks ago
samuel.channon
• 0
1
vote
11
replies
1.1k
views
DESeq2 gene length normalisation
Normalization
DESeq2
updated 7 months ago by
Michael Love
42k • written 7 months ago by
cm15245
• 0
1
vote
6
replies
464
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 7 weeks ago by
Michael Love
42k • written 7 weeks ago by
RL
• 0
1
vote
3
replies
643
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 4 months ago by
georgii.vdovin
• 0
1
vote
1
reply
468
views
DESeq2 Normalization for QC Samples
DESeq2
Normalization
updated 4 months ago by
Michael Love
42k • written 4 months ago by
phmai1148
• 0
1
vote
5
replies
1.1k
views
Does voom normalization quantile create difference in DGE genes when distribution of patients is similar (no big differences in quantiles)?
limmaGUI
normalization
limma
voom
Normalization
updated 10 months ago by
Gordon Smyth
50k • written 11 months ago by
manuelsokolov
• 0
1
vote
1
reply
100
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 6 days ago by
James W. MacDonald
66k • written 6 days ago by
Đình Vinh
• 0
1
vote
4
replies
2.7k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray
Preprocessing
NimbleGen
Normalization
written 18 months ago by
Sarah
• 0
0
votes
1
reply
124
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 17 days ago by
ATpoint
★ 4.2k • written 17 days ago by
sajadahmad41454
• 0
0
votes
1
reply
1.5k
views
EdgeR norm.factor input
Normalization
edgeR
Normalization
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 10.3 years ago by
Guest User
★ 13k
0
votes
0
replies
304
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
7 months ago
Florian
• 0
0
votes
0
replies
275
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization
SomaticSignatures
6 months ago
vasily.dobrovolsky
• 0
0
votes
1
reply
344
views
WGCNA Soft Power
Normalization
DESeq2
Network
RNASeqData
updated 4 months ago by
ATpoint
★ 4.2k • written 4 months ago by
Ömür Koray
• 0
0
votes
2
replies
1.6k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 16 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
0
votes
1
reply
58
views
Normalisation using clinical traits in RNA seq using DESeq2
DESeq2
clinicaltraits
Normalization
batchnormalisation
updated 18 hours ago by
ATpoint
★ 4.2k • written 2 days ago by
sukeshinik5
• 0
0
votes
2
replies
2.4k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 9 months ago by
manuel.fernandez
• 0 • written 2.1 years ago by
cicely.day
• 0
0
votes
6
replies
936
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
7 months ago
erika.maldonado-rosado
• 0
0
votes
3
replies
625
views
Normalization of different input materials
Normalization
DESeq2
updated 11 months ago by
ATpoint
★ 4.2k • written 11 months ago by
altuda
▴ 10
0
votes
2
replies
789
views
Can VST-transformed community composition data be expressed as relative abundance?
vst
relativeabundance
Normalization
DESeq2
12 months ago • updated 11 months ago
dwas
• 0
0
votes
1
reply
125
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 12 days ago by
Michael Love
42k • written 13 days ago by
piemmea
• 0
0
votes
0
replies
182
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
11 weeks ago • updated 9 weeks ago
Giovanni Calice
▴ 160
0
votes
2
replies
203
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
7 weeks ago
Marianna
▴ 20
0
votes
3
replies
2.5k
views
Background correction with neqc
Normalization
Cancer
Normalization
Cancer
updated 6 months ago by
Gordon Smyth
50k • written 12.5 years ago by
Guest User
★ 13k
34 results • Page
1 of 1
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Replies
Comment: ChAMP not available for bioconductor 3.19
by
Macsue
• 0
> if (!require("BiocManager", quietly = TRUE)) + install.packages("BiocManager") Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
BioinfGuru
▴ 30
I would use biomaRt. This is what happens when annotation occurs to early. If possible I would run the DEG analysis on the original output…
Comment: Volcano plot of scRNA-seq data not "centered"
by
ATpoint
★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0
by
Maximus
• 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered"
by
tjl
• 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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kevin.rue
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★ 3.6k
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50k
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