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Showing :
Normalization
•
reset
2
votes
2
replies
384
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
22 days ago • updated 21 days ago
Henry
▴ 10
1
vote
6
replies
430
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
RL
• 0
0
votes
2
replies
166
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
4 weeks ago
Marianna
▴ 20
1
vote
4
replies
290
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
6 weeks ago
samuel.channon
• 0
0
votes
0
replies
147
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
8 weeks ago • updated 6 weeks ago
Giovanni Calice
▴ 160
6
votes
11
replies
4.0k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 7 weeks ago by
Priya
• 0 • written 3.2 years ago by
Marina
▴ 40
2
votes
1
reply
296
views
Normalization factors when there is a possible unidirectional expression
limma
Normalization
DifferentialExpression
updated 11 weeks ago by
ATpoint
★ 4.1k • written 11 weeks ago by
Shaimaa Gamal
• 0
2
votes
2
replies
408
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
12 weeks ago
jackafiore
• 0
2
votes
3
replies
366
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 12 weeks ago by
James W. MacDonald
65k • written 12 weeks ago by
Shaimaa Gamal
• 0
1
vote
3
replies
577
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 3 months ago by
georgii.vdovin
• 0
0
votes
1
reply
295
views
WGCNA Soft Power
Normalization
DESeq2
Network
RNASeqData
updated 3 months ago by
ATpoint
★ 4.1k • written 3 months ago by
Ömür Koray
• 0
2
votes
4
replies
584
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
3 months ago
Sabiha
▴ 20
1
vote
1
reply
413
views
DESeq2 Normalization for QC Samples
DESeq2
Normalization
updated 3 months ago by
Michael Love
41k • written 3 months ago by
phmai1148
• 0
2
votes
2
replies
632
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2
medianofratiostransformation
StatisticalMethod
Normalization
dispersion
4 months ago • updated 3 months ago
Linton
• 0
0
votes
1
reply
1.5k
views
EdgeR norm.factor input
Normalization
edgeR
Normalization
edgeR
updated 4 months ago by
Gordon Smyth
50k • written 10.2 years ago by
Guest User
★ 13k
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
0
votes
0
replies
250
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization
SomaticSignatures
5 months ago
vasily.dobrovolsky
• 0
0
votes
3
replies
2.5k
views
Background correction with neqc
Normalization
Cancer
Normalization
Cancer
updated 6 months ago by
Gordon Smyth
50k • written 12.4 years ago by
Guest User
★ 13k
0
votes
6
replies
849
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
6 months ago
erika.maldonado-rosado
• 0
2
votes
5
replies
11k
views
Conversion from counts to FPKM
counts
fpkm
fpkm()
normalization
deseq2
updated 6 months ago by
Hamza
• 0 • written 5.4 years ago by
chiara.facciotto
• 0
0
votes
0
replies
279
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
6 months ago
Florian
• 0
1
vote
11
replies
1.0k
views
DESeq2 gene length normalisation
Normalization
DESeq2
updated 6 months ago by
Michael Love
41k • written 6 months ago by
cm15245
• 0
1
vote
4
replies
2.5k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray
Preprocessing
NimbleGen
Normalization
written 17 months ago by
Sarah
• 0
0
votes
2
replies
2.3k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 8 months ago by
manuel.fernandez
• 0 • written 2.1 years ago by
cicely.day
• 0
1
vote
6
replies
1.7k
views
can negative value microarray matrix data analysed by limma directly
limma
microarray
normalization
updated 8 months ago by
Gordon Smyth
50k • written 3.6 years ago by
linouhao
▴ 20
1
vote
5
replies
1.0k
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 10 months ago by
manuelsokolov
• 0
0
votes
3
replies
609
views
Normalization of different input materials
Normalization
DESeq2
updated 10 months ago by
ATpoint
★ 4.1k • written 10 months ago by
altuda
▴ 10
0
votes
2
replies
755
views
Can VST-transformed community composition data be expressed as relative abundance?
vst
relativeabundance
Normalization
DESeq2
11 months ago
dwas
• 0
5
votes
11
replies
3.0k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 11 months ago by
Sabiha
▴ 20
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 11 months ago by
Gordon Smyth
50k • written 17 months ago by
Sabiha
▴ 20
0
votes
3
replies
713
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq
normalization
PCR_efficiency
bias
intrasample_comparison
updated 11 months ago by
James W. MacDonald
65k • written 11 months ago by
FedeXander
• 0
1
vote
2
replies
899
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
12 months ago
Abdul
▴ 20
2
votes
2
replies
665
views
Question about transforming log expression values to antilog values in limma
IlluminaChip
limma
AffymetrixChip
Normalization
Microarray
13 months ago
Abdul
▴ 20
2
votes
6
replies
2.4k
views
RNA-seq analysis across different experiments
limma
deseq2
normalization
degenes
design and contrast matrix
written 6.8 years ago by
mrigaya.mehra
▴ 10
1
vote
2
replies
621
views
RNA-Seq normalization of pre and post treatment groups
Normalization
RNASeq
written 13 months ago by
Sarah
• 0
0
votes
2
replies
713
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran
Clustering
SingleCell
Normalization
13 months ago
Assa Yeroslaviz
★ 1.5k
2
votes
3
replies
1.8k
views
deseq2 normalization and statistical method
normalization
deseq2
StatisticalMethod
updated 13 months ago by
ATpoint
★ 4.1k • written 13 months ago by
SH
• 0
2
votes
3
replies
893
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 13 months ago by
ATpoint
★ 4.1k • written 13 months ago by
suphamon.j
▴ 20
9
votes
10
replies
6.8k
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization
edgeR
RPKM
updated 13 months ago by
Chris
• 0 • written 3.5 years ago by
anikng
▴ 10
0
votes
5
replies
1.2k
views
DESeq Normalization and miRNAs Filtering
DESeq2
Normalization
updated 13 months ago by
ATpoint
★ 4.1k • written 13 months ago by
phmai1148
• 0
1
vote
1
reply
991
views
deseq2 RLE normalization
RLE
normalization
deseq2
updated 13 months ago by
ATpoint
★ 4.1k • written 13 months ago by
SH
• 0
0
votes
1
reply
546
views
Using DESeq2 only for normalization
DESeq2
Normalization
updated 13 months ago by
ATpoint
★ 4.1k • written 13 months ago by
phmai1148
• 0
0
votes
1
reply
411
views
processing samples with significantly different counts
DESeq2
Normalization
updated 13 months ago by
ATpoint
★ 4.1k • written 13 months ago by
Anastasiia
• 0
0
votes
2
replies
1.0k
views
best way to normalize for differences in sample read depth: normalize genome vs cn.MOPs
cn.mops
normalization
updated 13 months ago by
yr542
• 0 • written 6.1 years ago by
znl207
• 0
0
votes
1
reply
540
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2
Normalization
sva
updated 14 months ago by
ATpoint
★ 4.1k • written 14 months ago by
marslena
• 0
0
votes
2
replies
736
views
Using Multi-Dimensional Scaling (MDS) to produce a vector in order to account for patient bias when constructing DGE lists from RNA-seq datasets in R?
PrincipalComponent
StatisticalMethod
edgeR
MultidimensionalScaling
Normalization
14 months ago
rcreswell01
• 0
3
votes
3
replies
803
views
What is cpmByGroup used for?
edgeR
Normalization
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
EM
• 0
4
votes
7
replies
2.0k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq
LongRead
Normalization
ShortRead
IlluminaRNASeq
15 months ago • updated 14 months ago
Bernardo
▴ 10
1
vote
1
reply
770
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR
SequencingData
miRNA
TMM
Normalization
updated 15 months ago by
Gordon Smyth
50k • written 15 months ago by
tleona3
• 0
4
votes
2
replies
1.7k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2
SpikeIn
Normalization
DifferentialExpression
updated 15 months ago by
ATpoint
★ 4.1k • written 15 months ago by
kalavattam
▴ 10
50 results • Page
1 of 1
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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. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
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…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
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
A: Print Differentially Expressed Exons From Dexseq Results
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