Showing : normalization • reset
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
3 days ago • updated 6 hours ago sukeshinik5 • 0
1
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1
reply
103
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 6 days ago by 66k • written 7 days ago by • 0
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1
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127
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 12 days ago by 42k • written 13 days ago by • 0
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2
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1.6k
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How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 17 days ago by • 0 • written 16 months ago by ▴ 10
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1
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124
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 18 days ago by ★ 4.2k • written 18 days ago by • 0
2
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2
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433
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
6 weeks ago Henry ▴ 10
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6
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464
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
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2
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203
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
7 weeks ago Marianna ▴ 20
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4
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330
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
9 weeks ago samuel.channon • 0
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182
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
11 weeks ago • updated 9 weeks ago Giovanni Calice ▴ 160
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11
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4.1k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 10 weeks ago by • 0 • written 3.2 years ago by ▴ 40
2
votes
1
reply
327
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 3 months ago by ★ 4.2k • written 3 months ago by • 0
2
votes
2
replies
453
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
2
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3
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403
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 66k • written 3 months ago by • 0
1
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3
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644
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 4 months ago by • 0
0
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1
reply
346
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 4 months ago by ★ 4.2k • written 4 months ago by • 0
2
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4
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671
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
1
vote
1
reply
468
views
DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 4 months ago by 42k • written 4 months ago by • 0
2
votes
2
replies
751
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
4 months ago Linton • 0
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1
reply
1.5k
views
EdgeR norm.factor input
Normalization edgeR Normalization edgeR
updated 5 months ago by 50k • written 10.3 years ago by ★ 13k
4
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4
replies
2.1k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 5 months ago by 50k • written 2.4 years ago by ▴ 10
0
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0
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276
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
6 months ago vasily.dobrovolsky • 0
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3
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2.5k
views
Background correction with neqc
Normalization Cancer Normalization Cancer
updated 6 months ago by 50k • written 12.5 years ago by ★ 13k
0
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6
replies
938
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
7 months ago erika.maldonado-rosado • 0
2
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5
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11k
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Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 7 months ago by • 0 • written 5.5 years ago by • 0
0
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0
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305
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
7 months ago Florian • 0
1
vote
11
replies
1.1k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 7 months ago by 42k • written 7 months ago by • 0
1
vote
4
replies
2.8k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 18 months ago by • 0
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2
replies
2.4k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 9 months ago by • 0 • written 2.1 years ago by • 0
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 50k • written 3.7 years ago by ▴ 20
1
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5
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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 50k • written 11 months ago by • 0
0
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3
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626
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Normalization of different input materials
Normalization DESeq2
updated 11 months ago by ★ 4.2k • written 11 months ago by ▴ 10
0
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2
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792
views
Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
12 months ago dwas • 0
5
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11
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3.2k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 12 months ago by ▴ 20
4
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8
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2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 12 months ago by 50k • written 18 months ago by ▴ 20
0
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3
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754
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 66k • written 12 months ago by • 0
1
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2
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919
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
13 months ago Abdul ▴ 20
2
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2
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687
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
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2.5k
views
RNA-seq analysis across different experiments
limma deseq2 normalization degenes design and contrast matrix
written 6.8 years ago by ▴ 10
1
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2
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629
views
RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 14 months ago by • 0
0
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2
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773
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
14 months ago Assa Yeroslaviz ★ 1.5k
2
votes
3
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1.9k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
2
votes
3
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945
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 14 months ago by ★ 4.2k • written 14 months ago by ▴ 20
9
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10
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7.0k
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 14 months ago by ▴ 10 • written 3.6 years ago by ▴ 10
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5
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1.3k
views
DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
1
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1
reply
1.0k
views
deseq2 RLE normalization
RLE normalization deseq2
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
0
votes
1
reply
569
views
Using DESeq2 only for normalization
DESeq2 Normalization
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
0
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1
reply
424
views
processing samples with significantly different counts
DESeq2 Normalization
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
0
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2
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1.0k
views
best way to normalize for differences in sample read depth: normalize genome vs cn.MOPs
cn.mops normalization
updated 14 months ago by • 0 • written 6.2 years ago by • 0
0
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1
reply
569
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
50 results • Page 1 of 1
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Comment: GSVA function by Robert Castelo ★ 3.3k
No, negative values may occur after log transformation when the `log(x)` is taken from a positive number `x with 0 < x < 1`, and therefore …
Comment: conumee with Infinium MethylationEPIC v2.0 by sgomez • 0
Hi Max, Could you try this? https://support.bioconductor.org/p/9136138/#9136840
Comment: Error in render R qmd document (could not find function "process") by ATpoint ★ 4.2k
This is not related to Bioconductor, and even if it was, please understand that without code one cannot debug these questions. The most obv…
Comment: GSVA function by michelafrancesconi8 • 0
When I log trasform my matrix after the DESeq2 normalization, I have some negative value, should I add a 1 to all my matrix? Thank you Mi…
Comment: Normalisation using clinical traits in RNA seq using DESeq2 by sukeshinik5 • 0
Thank you, so much for the response. When we estimate factors of unwanted variable, which is the better options for factorisation of the va…
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DiffBind Batch Effect
A: DiffBind Batch Effect
A: DiffBind Batch Effect
C: DiffBind Batch Effect
C: DiffBind Batch Effect
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