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Showing :
Normalization
•
reset
2
votes
2
replies
392
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
27 days ago • updated 26 days ago
Henry
▴ 10
1
vote
6
replies
440
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 4 weeks ago by
Michael Love
42k • written 5 weeks ago by
RL
• 0
0
votes
2
replies
176
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
5 weeks ago
Marianna
▴ 20
1
vote
4
replies
296
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
7 weeks ago • updated 6 weeks ago
samuel.channon
• 0
0
votes
0
replies
155
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
9 weeks ago • updated 7 weeks ago
Giovanni Calice
▴ 160
2
votes
1
reply
305
views
Normalization factors when there is a possible unidirectional expression
limma
Normalization
DifferentialExpression
updated 11 weeks ago by
ATpoint
★ 4.1k • written 12 weeks ago by
Shaimaa Gamal
• 0
2
votes
2
replies
415
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
3 months ago
jackafiore
• 0
2
votes
3
replies
374
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
Shaimaa Gamal
• 0
1
vote
3
replies
589
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
308
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
601
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
420
views
DESeq2 Normalization for QC Samples
DESeq2
Normalization
updated 4 months ago by
Michael Love
42k • written 4 months ago by
phmai1148
• 0
2
votes
2
replies
649
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2
medianofratiostransformation
StatisticalMethod
Normalization
dispersion
4 months ago
Linton
• 0
0
votes
0
replies
251
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization
SomaticSignatures
5 months ago
vasily.dobrovolsky
• 0
0
votes
6
replies
868
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
6 months ago
erika.maldonado-rosado
• 0
0
votes
0
replies
286
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
6 months ago
Florian
• 0
1
vote
11
replies
1.1k
views
DESeq2 gene length normalisation
Normalization
DESeq2
updated 6 months ago by
Michael Love
42k • written 7 months ago by
cm15245
• 0
1
vote
4
replies
2.6k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray
Preprocessing
NimbleGen
Normalization
written 17 months ago by
Sarah
• 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 10 months ago by
manuelsokolov
• 0
0
votes
3
replies
615
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
762
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
3.1k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 11 months ago by
Sabiha
▴ 20
0
votes
3
replies
719
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 12 months ago by
James W. MacDonald
65k • written 12 months ago by
FedeXander
• 0
1
vote
2
replies
902
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
13 months ago
Abdul
▴ 20
2
votes
2
replies
673
views
Question about transforming log expression values to antilog values in limma
IlluminaChip
limma
AffymetrixChip
Normalization
Microarray
13 months ago
Abdul
▴ 20
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
723
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran
Clustering
SingleCell
Normalization
13 months ago
Assa Yeroslaviz
★ 1.5k
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 3.6 years ago by
linouhao
▴ 20
2
votes
3
replies
1.9k
views
deseq2 normalization and statistical method
normalization
deseq2
StatisticalMethod
updated 13 months ago by
ATpoint
★ 4.1k • written 13 months ago by
SH
• 0
1
vote
1
reply
999
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
549
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
415
views
processing samples with significantly different counts
DESeq2
Normalization
updated 13 months ago by
ATpoint
★ 4.1k • written 14 months ago by
Anastasiia
• 0
0
votes
5
replies
1.2k
views
DESeq Normalization and miRNAs Filtering
DESeq2
Normalization
updated 13 months ago by
ATpoint
★ 4.1k • written 14 months ago by
phmai1148
• 0
2
votes
3
replies
898
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 13 months ago by
ATpoint
★ 4.1k • written 14 months ago by
suphamon.j
▴ 20
0
votes
1
reply
543
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
3
votes
3
replies
806
views
What is cpmByGroup used for?
edgeR
Normalization
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
EM
• 0
0
votes
2
replies
739
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
1
vote
1
reply
775
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
0
votes
1
reply
637
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 15 months ago by
James W. MacDonald
65k • written 15 months ago by
Aleksandra
• 0
0
votes
1
reply
1.3k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 15 months ago by
Michael Love
42k • written 15 months ago by
kalavattam
▴ 10
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
Bernardo
▴ 10
1
vote
0
replies
578
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn
vsn
Normalization
vsn2
Proteomics
16 months ago
Arend
▴ 10
0
votes
0
replies
738
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
16 months ago
Zhijie
• 0
1
vote
0
replies
677
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran
Normalization
scRNA
BatchEffect
16 months ago
r_grau
▴ 10
3
votes
4
replies
1.6k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind
SpikeIn
Normalization
ChIP-seq
csaw
17 months ago • updated 16 months ago
spg
• 0
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
1
reply
634
views
TCGA RNAseq Normalization
normalization
RNASEQ
Normalization
TCGAutils
TCGA
updated 17 months ago by
ATpoint
★ 4.1k • written 17 months ago by
Deniz
• 0
0
votes
2
replies
1000
views
Deseq2 and co-expression network normalization
DESeq2
Normalization
DifferentialExpression
r
updated 17 months ago by
ATpoint
★ 4.1k • written 17 months ago by
lola
• 0
2
votes
4
replies
3.5k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2
R
edgeR
Normalization
RNASeq
17 months ago
mohammedtoufiq91
▴ 10
50 results • Page
1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results
by
swbarnes2
★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Mike Smith
★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data
by
Robert Castelo
★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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