Showing : Normalization • reset
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gene detection across experiments
DESeq2 Normalization
7 weeks ago • updated 6 weeks ago Mara • 0
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3
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1.5k
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RNA-seq: TPM batch effect correction
rnaseqDTU Normalization
updated 7 weeks ago by 68k • written 7 weeks ago by • 0
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5
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669
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WGCNA
WGCNA Normalization RNASeq
written 5 months ago by • 0
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2
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446
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Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis Normalization Epigenetics MethylationArrayData
6 months ago a.alkema • 0
6
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5
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934
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 7 months ago by 68k • written 7 months ago by • 0
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0
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294
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Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization Lipidomics lipidr
8 months ago David R ▴ 90
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4
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1.1k
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
9 months ago dseauer • 0
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2
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1.3k
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
9 months ago Ai • 0
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0
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494
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Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
9 months ago kim • 0
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1
reply
810
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 9 months ago by ★ 4.9k • written 9 months ago by • 0
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1.1k
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
10 months ago Eva ▴ 10
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488
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Background normalization of Diffbind dba.normalize
Normalization DiffBind
10 months ago Young Boqin • 0
1
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1
reply
484
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 10 months ago by ★ 4.9k • written 10 months ago by • 0
1
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5
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1.3k
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 11 months ago by 52k • written 12 months ago by • 0
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2
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588
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 12 months ago by • 0
1
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3
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1.8k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
14 months ago Tanvi • 0
2
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2
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788
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 14 months ago by ▴ 10 • written 15 months ago by • 0
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2
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888
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
15 months ago • updated 14 months ago sukeshinik5 ▴ 20
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1
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668
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 15 months ago by 43k • written 15 months ago by • 0
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1
reply
652
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 15 months ago by ★ 4.9k • written 15 months ago by • 0
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2
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1.6k
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
16 months ago Henry ▴ 10
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6
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1.5k
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 16 months ago by 43k • written 16 months ago by • 0
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830
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
16 months ago Marianna ▴ 20
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1.0k
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
17 months ago samuel.channon • 0
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559
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
17 months ago Giovanni Calice ▴ 160
2
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1
reply
711
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 18 months ago by ★ 4.9k • written 18 months ago by • 0
2
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2
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1.6k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
18 months ago jackafiore • 0
2
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3
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969
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 18 months ago by 68k • written 18 months ago by • 0
1
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3
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1.2k
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 18 months ago by • 0
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1
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1.0k
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WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 19 months ago by ★ 4.9k • written 19 months ago by • 0
2
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4
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2.0k
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
19 months ago Sabiha ▴ 20
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969
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DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 19 months ago by 43k • written 19 months ago by • 0
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DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
19 months ago Linton • 0
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0
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724
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
21 months ago vasily.dobrovolsky • 0
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6
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2.2k
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
22 months ago erika.maldonado-rosado • 0
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0
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671
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
22 months ago Florian • 0
1
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11
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2.7k
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DESeq2 gene length normalisation
Normalization DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
1
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4
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5.6k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 2.7 years ago by • 0
1
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5
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1.9k
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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 2.1 years ago by 52k • written 2.1 years ago by • 0
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3
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1.1k
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Normalization of different input materials
Normalization DESeq2
updated 2.1 years ago by ★ 4.9k • written 2.1 years ago by ▴ 10
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1.4k
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Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
2.2 years ago dwas • 0
5
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11
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7.2k
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Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 2.2 years ago by ▴ 20
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3
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1.2k
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 2.3 years ago by 68k • written 2.3 years ago by • 0
1
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2
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1.6k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
2.3 years ago Abdul ▴ 20
2
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2
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1.1k
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
2.4 years ago Abdul ▴ 20
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2
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959
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 2.4 years ago by • 0
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2
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1.5k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.4 years ago Assa Yeroslaviz ★ 1.5k
1
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6
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2.9k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 2.0 years ago by 52k • written 4.9 years ago by ▴ 20
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3
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3.5k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 2.4 years ago by ★ 4.9k • written 2.4 years ago by ▴ 10
2
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1
reply
1.9k
views
deseq2 RLE normalization
RLE normalization deseq2
updated 2.4 years ago by ★ 4.9k • written 2.4 years ago by ▴ 10
1,761 results • Page 1 of 36
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Comment: EuroBioC2024 abstract submission is open! by rajilrfaze • 0
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Comment: p-adjusted values in multiple comparisons by ocanorocabayera • 0
Thank you Gordon for your thorough reply. It seems when MDS-plotting the obtained object from 'voom', that the points do not cluster togeth…
Comment: Are voomByGroup and voomLmFit compatible? by Gordon Smyth 52k
Not sure what "points" you are referring to, or what you mean by them being "weighted".
Answer: p-adjusted values in multiple comparisons by Gordon Smyth 52k
If your data was completely random, with no truly differentially expressed (DE) genes, then you would expect to get nearly 5% of the p-valu…
Answer: Are voomByGroup and voomLmFit compatible? by Gordon Smyth 52k
voomByGroup isn't part of Bioconductor, so questions about it should be send to the voomByGroup issues page. I haven't brought voomByGroup…
Votes
Answer: p-adjusted values in multiple comparisons
Comment: Very different log2 Fold changes with DESeq2 and explict calculation
Answer: (Why) do limma's confidence intervals depend on topTable's p.value argument?
Answer: (Why) do limma's confidence intervals depend on topTable's p.value argument?
Answer: Very different log2 Fold changes with DESeq2 and explict calculation
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