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Showing :
Normalization
•
reset
0
votes
0
replies
115
views
Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization
Lipidomics
lipidr
26 days ago
David R
▴ 90
3
votes
4
replies
622
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization
limma
within-arraynormalisation
Printerlayout
5 weeks ago
dseauer
• 0
1
vote
2
replies
932
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma
MicroarrayData
Normalization
6 weeks ago
Ai
• 0
0
votes
0
replies
157
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
6 weeks ago
kim
• 0
0
votes
1
reply
366
views
Spike-in normalization method in ATACseq
sperm
Drosophila_melanogaster
ATACSeq
Normalization
SpikeIn
updated 6 weeks ago by
ATpoint
★ 4.6k • written 7 weeks ago by
Katerina
• 0
3
votes
4
replies
526
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization
DESeq2
rlog
vst
10 weeks ago
Eva
▴ 10
0
votes
0
replies
169
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
10 weeks ago
Young Boqin
• 0
1
vote
1
reply
254
views
Normalization RNA-seq for multiple plates
Normalization
DESeq2
RNASeqData
edgeR
updated 11 weeks ago by
ATpoint
★ 4.6k • written 11 weeks ago by
Pimpa
• 0
1
vote
5
replies
840
views
RNASeq normlization for samples with global shift in gene expression
qsmooth
DESeq2
limma
Normalization
updated 3 months ago by
Gordon Smyth
52k • written 4 months ago by
Xuan Yi
• 0
0
votes
2
replies
358
views
Analysis of transcription inhibition with DESeq2
SpikeIn
DESeq2
Normalization
written 4 months ago by
ADopico
• 0
1
vote
3
replies
968
views
Combining two bulk RNA seq datasets
RNASeqData
DESeq2
Normalization
6 months ago
Tanvi
• 0
2
votes
2
replies
536
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 6 months ago by
jessica.mcclintock
▴ 10 • written 7 months ago by
Đình Vinh
• 0
0
votes
2
replies
556
views
Normalisation using clinical traits in RNA seq using DESeq2
DESeq2
clinicaltraits
Normalization
batchnormalisation
7 months ago • updated 6 months ago
sukeshinik5
▴ 20
0
votes
1
reply
407
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 7 months ago by
Michael Love
43k • written 7 months ago by
piemmea
• 0
0
votes
1
reply
392
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 7 months ago by
ATpoint
★ 4.6k • written 7 months ago by
sajadahmad41454
• 0
2
votes
2
replies
987
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
8 months ago
Henry
▴ 10
1
vote
6
replies
884
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 8 months ago by
Michael Love
43k • written 8 months ago by
RL
• 0
0
votes
2
replies
548
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
8 months ago
Marianna
▴ 20
1
vote
4
replies
689
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
9 months ago
samuel.channon
• 0
0
votes
0
replies
399
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
9 months ago
Giovanni Calice
▴ 160
2
votes
1
reply
529
views
Normalization factors when there is a possible unidirectional expression
limma
Normalization
DifferentialExpression
updated 10 months ago by
ATpoint
★ 4.6k • written 10 months ago by
Shaimaa Gamal
• 0
2
votes
2
replies
1.0k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
10 months ago
jackafiore
• 0
2
votes
3
replies
690
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 10 months ago by
James W. MacDonald
67k • written 10 months ago by
Shaimaa Gamal
• 0
1
vote
3
replies
987
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics
Normalization
RNASeq
DESeq2
written 11 months ago by
georgii.vdovin
• 0
0
votes
1
reply
745
views
WGCNA Soft Power
Normalization
DESeq2
Network
RNASeqData
updated 11 months ago by
ATpoint
★ 4.6k • written 11 months ago by
Ömür Koray
• 0
2
votes
4
replies
1.5k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
11 months ago
Sabiha
▴ 20
1
vote
1
reply
742
views
DESeq2 Normalization for QC Samples
DESeq2
Normalization
updated 11 months ago by
Michael Love
43k • written 11 months ago by
phmai1148
• 0
2
votes
2
replies
2.0k
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2
medianofratiostransformation
StatisticalMethod
Normalization
dispersion
11 months ago
Linton
• 0
0
votes
0
replies
502
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization
SomaticSignatures
13 months ago
vasily.dobrovolsky
• 0
0
votes
6
replies
1.6k
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
14 months ago
erika.maldonado-rosado
• 0
0
votes
0
replies
514
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
14 months ago
Florian
• 0
1
vote
11
replies
1.9k
views
DESeq2 gene length normalisation
Normalization
DESeq2
updated 14 months ago by
Michael Love
43k • written 14 months ago by
cm15245
• 0
1
vote
4
replies
4.2k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray
Preprocessing
NimbleGen
Normalization
written 2.1 years ago by
Sarah
• 0
1
vote
5
replies
1.5k
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 17 months ago by
Gordon Smyth
52k • written 17 months ago by
manuelsokolov
• 0
0
votes
3
replies
868
views
Normalization of different input materials
Normalization
DESeq2
updated 18 months ago by
ATpoint
★ 4.6k • written 18 months ago by
altuda
▴ 10
0
votes
2
replies
1.1k
views
Can VST-transformed community composition data be expressed as relative abundance?
vst
relativeabundance
Normalization
DESeq2
18 months ago
dwas
• 0
5
votes
11
replies
5.1k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 19 months ago by
Sabiha
▴ 20
0
votes
3
replies
998
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 19 months ago by
James W. MacDonald
67k • written 19 months ago by
FedeXandeR
• 0
1
vote
2
replies
1.3k
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
20 months ago
Abdul
▴ 20
2
votes
2
replies
896
views
Question about transforming log expression values to antilog values in limma
IlluminaChip
limma
AffymetrixChip
Normalization
Microarray
20 months ago
Abdul
▴ 20
1
vote
2
replies
813
views
RNA-Seq normalization of pre and post treatment groups
Normalization
RNASeq
written 20 months ago by
Sarah
• 0
0
votes
2
replies
1.1k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran
Clustering
SingleCell
Normalization
21 months ago
Assa Yeroslaviz
★ 1.5k
1
vote
6
replies
2.4k
views
can negative value microarray matrix data analysed by limma directly
limma
microarray
normalization
updated 16 months ago by
Gordon Smyth
52k • written 4.3 years ago by
linouhao
▴ 20
2
votes
3
replies
2.8k
views
deseq2 normalization and statistical method
normalization
deseq2
StatisticalMethod
updated 21 months ago by
ATpoint
★ 4.6k • written 21 months ago by
SH
▴ 10
2
votes
1
reply
1.5k
views
deseq2 RLE normalization
RLE
normalization
deseq2
updated 21 months ago by
ATpoint
★ 4.6k • written 21 months ago by
SH
▴ 10
0
votes
1
reply
882
views
Using DESeq2 only for normalization
DESeq2
Normalization
updated 21 months ago by
ATpoint
★ 4.6k • written 21 months ago by
phmai1148
• 0
0
votes
1
reply
595
views
processing samples with significantly different counts
DESeq2
Normalization
updated 21 months ago by
ATpoint
★ 4.6k • written 21 months ago by
Anastasiia
• 0
0
votes
5
replies
1.8k
views
DESeq Normalization and miRNAs Filtering
DESeq2
Normalization
updated 21 months ago by
ATpoint
★ 4.6k • written 21 months ago by
phmai1148
• 0
2
votes
3
replies
1.3k
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 21 months ago by
ATpoint
★ 4.6k • written 21 months ago by
suphamon.j
▴ 20
0
votes
1
reply
800
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2
Normalization
sva
updated 21 months ago by
ATpoint
★ 4.6k • written 21 months ago by
marslena
• 0
50 results • Page
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Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
xiaofeiwang198266
• 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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