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Showing :
normalization
•
reset
2
votes
2
replies
362
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
15 days ago • updated 14 days ago
Henry
▴ 10
1
vote
6
replies
407
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 23 days ago by
Michael Love
41k • written 23 days ago by
RL
• 0
0
votes
2
replies
148
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
23 days ago
Marianna
▴ 20
1
vote
4
replies
272
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
5 weeks ago
samuel.channon
• 0
0
votes
0
replies
140
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
7 weeks ago • updated 5 weeks ago
Giovanni Calice
▴ 160
2
votes
1
reply
283
views
Normalization factors when there is a possible unidirectional expression
limma
Normalization
DifferentialExpression
updated 10 weeks ago by
ATpoint
★ 4.0k • written 10 weeks ago by
Shaimaa Gamal
• 0
2
votes
2
replies
386
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2
Normalization
RNASeq
11 weeks ago
jackafiore
• 0
2
votes
3
replies
355
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 11 weeks ago by
James W. MacDonald
65k • written 11 weeks ago by
Shaimaa Gamal
• 0
1
vote
3
replies
556
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
274
views
WGCNA Soft Power
Normalization
DESeq2
Network
RNASeqData
updated 3 months ago by
ATpoint
★ 4.0k • written 3 months ago by
Ömür Koray
• 0
2
votes
4
replies
553
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
399
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
597
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2
medianofratiostransformation
StatisticalMethod
Normalization
dispersion
3 months ago
Linton
• 0
0
votes
0
replies
241
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization
SomaticSignatures
5 months ago
vasily.dobrovolsky
• 0
0
votes
6
replies
815
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
6 months ago
erika.maldonado-rosado
• 0
0
votes
0
replies
268
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
6 months ago
Florian
• 0
1
vote
11
replies
997
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
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 9 months ago by
Gordon Smyth
50k • written 10 months ago by
manuelsokolov
• 0
0
votes
3
replies
596
views
Normalization of different input materials
Normalization
DESeq2
updated 10 months ago by
ATpoint
★ 4.0k • written 10 months ago by
altuda
▴ 10
0
votes
2
replies
739
views
Can VST-transformed community composition data be expressed as relative abundance?
vst
relativeabundance
Normalization
DESeq2
11 months ago • updated 10 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
0
votes
3
replies
702
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
876
views
Filter by expression and keep probes in limma
R
filter
limma
Normalization
Microarray
12 months ago
Abdul
▴ 20
2
votes
2
replies
655
views
Question about transforming log expression values to antilog values in limma
IlluminaChip
limma
AffymetrixChip
Normalization
Microarray
12 months ago
Abdul
▴ 20
1
vote
2
replies
610
views
RNA-Seq normalization of pre and post treatment groups
Normalization
RNASeq
written 13 months ago by
Sarah
• 0
0
votes
2
replies
700
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
1.7k
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
2
votes
3
replies
1.8k
views
deseq2 normalization and statistical method
normalization
deseq2
StatisticalMethod
updated 13 months ago by
ATpoint
★ 4.0k • written 13 months ago by
SH
• 0
1
vote
1
reply
972
views
deseq2 RLE normalization
RLE
normalization
deseq2
updated 13 months ago by
ATpoint
★ 4.0k • written 13 months ago by
SH
• 0
0
votes
1
reply
537
views
Using DESeq2 only for normalization
DESeq2
Normalization
updated 13 months ago by
ATpoint
★ 4.0k • written 13 months ago by
phmai1148
• 0
0
votes
1
reply
407
views
processing samples with significantly different counts
DESeq2
Normalization
updated 13 months ago by
ATpoint
★ 4.0k • written 13 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
★ 4.0k • written 13 months ago by
phmai1148
• 0
2
votes
3
replies
879
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 13 months ago by
ATpoint
★ 4.0k • written 13 months ago by
suphamon.j
▴ 20
0
votes
1
reply
534
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2
Normalization
sva
updated 13 months ago by
ATpoint
★ 4.0k • written 13 months ago by
marslena
• 0
3
votes
3
replies
790
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
726
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
752
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR
SequencingData
miRNA
TMM
Normalization
updated 14 months ago by
Gordon Smyth
50k • written 14 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 14 months ago by
ATpoint
★ 4.0k • written 14 months ago by
kalavattam
▴ 10
0
votes
1
reply
626
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
41k • 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 • updated 14 months ago
Bernardo
▴ 10
1
vote
0
replies
568
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn
vsn
Normalization
vsn2
Proteomics
15 months ago
Arend
▴ 10
0
votes
0
replies
721
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
15 months ago
Zhijie
• 0
1
vote
0
replies
658
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
16 months ago • updated 15 months ago
spg
• 0
4
votes
8
replies
2.1k
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
623
views
TCGA RNAseq Normalization
normalization
RNASEQ
Normalization
TCGAutils
TCGA
updated 17 months ago by
ATpoint
★ 4.0k • written 17 months ago by
Deniz
• 0
0
votes
2
replies
976
views
Deseq2 and co-expression network normalization
DESeq2
Normalization
DifferentialExpression
r
updated 17 months ago by
ATpoint
★ 4.0k • written 17 months ago by
lola
• 0
2
votes
4
replies
3.4k
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
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Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
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For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
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▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
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41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
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