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Showing :
Normalization
•
reset
0
votes
2
replies
981
views
gene detection across experiments
DESeq2
Normalization
5 months ago
Mara
• 0
0
votes
3
replies
1.7k
views
RNA-seq: TPM batch effect correction
rnaseqDTU
Normalization
updated 5 months ago by
James W. MacDonald
68k • written 5 months ago by
Samuel
• 0
0
votes
5
replies
885
views
WGCNA
WGCNA
Normalization
RNASeq
written 9 months ago by
Vishnu
• 0
0
votes
2
replies
527
views
Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis
Normalization
Epigenetics
MethylationArrayData
10 months ago
a.alkema
• 0
6
votes
5
replies
1.1k
views
How do I fix an odd voom plot in a combined dataset?
limma
Normalization
voom
updated 10 months ago by
James W. MacDonald
68k • written 11 months ago by
1sunmic2
• 0
0
votes
0
replies
370
views
Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization
Lipidomics
lipidr
12 months ago
David R
▴ 90
3
votes
4
replies
1.2k
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization
limma
within-arraynormalisation
Printerlayout
12 months ago
dseauer
• 0
1
vote
2
replies
1.4k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma
MicroarrayData
Normalization
13 months ago
Ai
• 0
0
votes
0
replies
590
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
13 months ago
kim
• 0
0
votes
1
reply
932
views
Spike-in normalization method in ATACseq
sperm
Drosophila_melanogaster
ATACSeq
Normalization
SpikeIn
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
Katerina
• 0
3
votes
4
replies
1.3k
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization
DESeq2
rlog
vst
13 months ago
Eva
▴ 10
0
votes
0
replies
617
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
13 months ago
Young Boqin
• 0
1
vote
1
reply
694
views
Normalization RNA-seq for multiple plates
Normalization
DESeq2
RNASeqData
edgeR
updated 14 months ago by
ATpoint
★ 5.0k • written 14 months ago by
Pimpa
• 0
1
vote
5
replies
1.5k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth
DESeq2
limma
Normalization
updated 15 months ago by
Gordon Smyth
53k • written 15 months ago by
Xuan Yi
• 0
0
votes
2
replies
684
views
Analysis of transcription inhibition with DESeq2
SpikeIn
DESeq2
Normalization
written 15 months ago by
ADopico
• 0
1
vote
3
replies
1.9k
views
Combining two bulk RNA seq datasets
RNASeqData
DESeq2
Normalization
17 months ago
Tanvi
• 0
2
votes
2
replies
882
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 18 months ago by
jessica.anderson
▴ 10 • written 18 months ago by
Đình Vinh
• 0
0
votes
2
replies
975
views
Normalisation using clinical traits in RNA seq using DESeq2
DESeq2
clinicaltraits
Normalization
batchnormalisation
18 months ago
sukeshinik5
▴ 20
0
votes
1
reply
765
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 18 months ago by
Michael Love
43k • written 18 months ago by
piemmea
• 0
0
votes
1
reply
722
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 19 months ago by
ATpoint
★ 5.0k • written 19 months ago by
sajadahmad41454
• 0
2
votes
2
replies
1.8k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
20 months ago • updated 19 months ago
Henry
▴ 10
1
vote
6
replies
1.6k
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 20 months ago by
Michael Love
43k • written 20 months ago by
RL
• 0
0
votes
2
replies
938
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
20 months ago
Marianna
▴ 20
1
vote
4
replies
1.1k
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
20 months ago
samuel.channon
• 0
0
votes
0
replies
615
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
21 months ago • updated 20 months ago
Giovanni Calice
▴ 160
2
votes
1
reply
799
views
Normalization factors when there is a possible unidirectional expression
limma
Normalization
DifferentialExpression
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
Shaimaa Gamal
• 0
2
votes
2
replies
1.7k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
22 months ago
jackafiore
• 0
2
votes
3
replies
1.1k
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 22 months ago by
James W. MacDonald
68k • written 22 months ago by
Shaimaa Gamal
• 0
1
vote
3
replies
1.3k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 22 months ago by
georgii.vdovin
• 0
0
votes
1
reply
1.2k
views
WGCNA Soft Power
Normalization
DESeq2
Network
RNASeqData
updated 22 months ago by
ATpoint
★ 5.0k • written 22 months ago by
Ömür Koray
• 0
2
votes
4
replies
2.2k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
22 months ago
Sabiha
▴ 20
1
vote
1
reply
1.0k
views
DESeq2 Normalization for QC Samples
DESeq2
Normalization
updated 23 months ago by
Michael Love
43k • written 23 months ago by
phmai1148
• 0
2
votes
2
replies
3.6k
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2
medianofratiostransformation
StatisticalMethod
Normalization
dispersion
23 months ago
Linton
• 0
0
votes
0
replies
812
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization
SomaticSignatures
2.0 years ago
vasily.dobrovolsky
• 0
0
votes
6
replies
2.3k
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
2.1 years ago
erika.maldonado-rosado
• 0
0
votes
0
replies
730
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
2.1 years ago
Florian
• 0
1
vote
11
replies
2.9k
views
DESeq2 gene length normalisation
Normalization
DESeq2
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
cm15245
• 0
1
vote
4
replies
6.0k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray
Preprocessing
NimbleGen
Normalization
written 3.0 years ago by
Sarah
• 0
1
vote
5
replies
2.0k
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 2.4 years ago by
Gordon Smyth
53k • written 2.4 years ago by
manuelsokolov
• 0
0
votes
3
replies
1.1k
views
Normalization of different input materials
Normalization
DESeq2
updated 2.4 years ago by
ATpoint
★ 5.0k • written 2.4 years ago by
altuda
▴ 10
0
votes
2
replies
1.5k
views
Can VST-transformed community composition data be expressed as relative abundance?
vst
relativeabundance
Normalization
DESeq2
2.5 years ago
dwas
• 0
5
votes
11
replies
7.5k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 2.5 years ago by
Sabiha
▴ 20
0
votes
3
replies
1.3k
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 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
FedeXandeR
• 0
1
vote
2
replies
1.7k
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
2.6 years ago
Abdul
▴ 20
2
votes
2
replies
1.2k
views
Question about transforming log expression values to antilog values in limma
IlluminaChip
limma
AffymetrixChip
Normalization
Microarray
2.7 years ago
Abdul
▴ 20
1
vote
2
replies
1.0k
views
RNA-Seq normalization of pre and post treatment groups
Normalization
RNASeq
written 2.7 years ago by
Sarah
• 0
0
votes
2
replies
1.6k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran
Clustering
SingleCell
Normalization
2.7 years ago
Assa Yeroslaviz
★ 1.5k
1
vote
6
replies
3.0k
views
can negative value microarray matrix data analysed by limma directly
limma
microarray
normalization
updated 2.3 years ago by
Gordon Smyth
53k • written 5.2 years ago by
linouhao
▴ 20
2
votes
3
replies
3.7k
views
deseq2 normalization and statistical method
normalization
deseq2
StatisticalMethod
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
SH
▴ 10
2
votes
1
reply
2.0k
views
deseq2 RLE normalization
RLE
normalization
deseq2
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
SH
▴ 10
1,761 results • Page
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Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR
by
efoss
▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma
by
Gordon Smyth
53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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