Showing : normalization • reset
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
2 days ago • updated 2 hours ago sukeshinik5 • 0
1
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1
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101
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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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125
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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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1
reply
124
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 17 days ago by ★ 4.2k • written 17 days ago by • 0
2
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2
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432
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
6 weeks ago Henry ▴ 10
1
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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
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
1
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4
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330
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
9 weeks ago samuel.channon • 0
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0
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182
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
11 weeks ago • updated 9 weeks ago Giovanni Calice ▴ 160
2
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1
reply
327
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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
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2
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453
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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
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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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643
views
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
344
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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670
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
1
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1
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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
748
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
4 months ago Linton • 0
0
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0
replies
275
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
6 months ago vasily.dobrovolsky • 0
0
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6
replies
937
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
7 months ago erika.maldonado-rosado • 0
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0
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304
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
7 months ago Florian • 0
1
vote
11
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1.1k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 7 months ago by 42k • written 7 months ago by • 0
1
vote
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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791
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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
0
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3
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752
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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
vote
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
votes
2
replies
687
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
13 months ago Abdul ▴ 20
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
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
14 months ago Assa Yeroslaviz ★ 1.5k
2
votes
3
replies
1.9k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
0
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1
reply
568
views
Using DESeq2 only for normalization
DESeq2 Normalization
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
1
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1
reply
1.0k
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deseq2 RLE normalization
RLE normalization deseq2
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
0
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5
replies
1.3k
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DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
0
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1
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423
views
processing samples with significantly different counts
DESeq2 Normalization
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
2
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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
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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
3
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3
replies
816
views
What is cpmByGroup used for?
edgeR Normalization
updated 15 months ago by 66k • written 15 months ago by • 0
0
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2
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760
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
15 months ago rcreswell01 • 0
1
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1
reply
801
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 15 months ago by 50k • written 15 months ago by • 0
4
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2
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1.8k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 15 months ago by ★ 4.2k • written 15 months ago by ▴ 10
0
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1
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653
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 16 months ago by 66k • written 16 months ago by • 0
4
votes
7
replies
2.1k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
16 months ago • updated 15 months ago Bernardo ▴ 10
0
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2
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1.6k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 16 days ago by • 0 • written 16 months ago by ▴ 10
1
vote
0
replies
590
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
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0
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762
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
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0
replies
696
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
17 months ago r_grau ▴ 10
3
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4
replies
1.7k
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 12 months ago by 50k • written 18 months ago by ▴ 20
0
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1
reply
646
views
TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 18 months ago by ★ 4.2k • written 18 months ago by • 0
50 results • Page 1 of 1
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Answer: ChAMP not available for bioconductor 3.19 by ATpoint ★ 4.2k
https://support.bioconductor.org/p/9158324/#9158336
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…
Comment: ChAMP not available for bioconductor 3.19 by Macsue • 0
Warning message:package ChAMP is not available for Bioconductor version 3.19 A version of this package for your version of R might be avail…
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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