Showing : normalization • reset
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WGCNA
WGCNA Normalization RNASeq
updated 12 weeks ago by • 0 • written 3 months ago by • 0
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2
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374
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Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis Normalization Epigenetics MethylationArrayData
3 months ago a.alkema • 0
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5
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809
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 4 months ago by 68k • written 4 months ago by • 0
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231
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Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization Lipidomics lipidr
5 months ago David R ▴ 90
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4
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924
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
6 months ago dseauer • 0
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2
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1.2k
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
6 months ago Ai • 0
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415
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Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
6 months ago kim • 0
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1
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718
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 6 months ago by ★ 4.8k • written 6 months ago by • 0
3
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4
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947
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
7 months ago Eva ▴ 10
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394
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Background normalization of Diffbind dba.normalize
Normalization DiffBind
7 months ago Young Boqin • 0
1
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1
reply
414
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 7 months ago by ★ 4.8k • written 7 months ago by • 0
1
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5
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1.2k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 8 months ago by 52k • written 9 months ago by • 0
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2
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523
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 9 months ago by • 0
1
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3
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1.6k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
11 months ago Tanvi • 0
2
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2
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702
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 11 months ago by ▴ 10 • written 12 months ago by • 0
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2
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816
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
12 months ago • updated 11 months ago sukeshinik5 ▴ 20
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1
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567
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 12 months ago by 43k • written 12 months ago by • 0
0
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1
reply
574
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 12 months ago by ★ 4.8k • written 12 months ago by • 0
2
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2
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1.4k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
13 months ago Henry ▴ 10
1
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6
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1.4k
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 13 months ago by 43k • written 13 months ago by • 0
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2
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733
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
13 months ago Marianna ▴ 20
1
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4
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911
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
14 months ago samuel.channon • 0
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508
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
14 months ago Giovanni Calice ▴ 160
2
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1
reply
638
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 15 months ago by ★ 4.8k • written 15 months ago by • 0
2
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2
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1.5k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
15 months ago jackafiore • 0
2
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3
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868
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 15 months ago by 68k • written 15 months ago by • 0
1
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3
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1.1k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 16 months ago by • 0
0
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1
reply
966
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 16 months ago by ★ 4.8k • written 16 months ago by • 0
2
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4
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1.9k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
16 months ago Sabiha ▴ 20
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1
reply
897
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DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 16 months ago by 43k • written 16 months ago by • 0
2
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2
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3.3k
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
16 months ago Linton • 0
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0
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641
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
18 months ago vasily.dobrovolsky • 0
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6
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2.1k
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
19 months ago erika.maldonado-rosado • 0
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624
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
19 months ago Florian • 0
1
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11
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2.6k
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DESeq2 gene length normalisation
Normalization DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
1
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4
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5.2k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 2.5 years ago by • 0
1
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5
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1.7k
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 22 months ago by 52k • written 23 months ago by • 0
0
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3
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991
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Normalization of different input materials
Normalization DESeq2
updated 23 months ago by ★ 4.8k • written 23 months ago by ▴ 10
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2
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1.3k
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Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
24 months ago • updated 23 months ago dwas • 0
5
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11
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6.9k
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Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 24 months ago by ▴ 20
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3
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1.1k
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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 2.0 years ago by 68k • written 2.0 years ago by • 0
1
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1.5k
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Filter by expression and keep probes in limma
R filter limma Normalization Microarray
2.1 years ago Abdul ▴ 20
2
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2
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1.0k
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
2.1 years ago Abdul ▴ 20
1
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2
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913
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 2.1 years ago by • 0
0
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2
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1.4k
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.1 years ago Assa Yeroslaviz ★ 1.5k
1
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6
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2.8k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 21 months ago by 52k • written 4.7 years ago by ▴ 20
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3
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3.4k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 2.2 years ago by ★ 4.8k • written 2.2 years ago by ▴ 10
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1
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1.8k
views
deseq2 RLE normalization
RLE normalization deseq2
updated 2.2 years ago by ★ 4.8k • written 2.2 years ago by ▴ 10
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1
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1.1k
views
Using DESeq2 only for normalization
DESeq2 Normalization
updated 2.2 years ago by ★ 4.8k • written 2.2 years ago by • 0
0
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1
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670
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processing samples with significantly different counts
DESeq2 Normalization
updated 2.2 years ago by ★ 4.8k • written 2.2 years ago by • 0
50 results • Page 1 of 1
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Comment: Heatmap of rnaseq data with z-score scale by James W. MacDonald 68k
`heatmap.2` is a CRAN package, and that's the relevant issue for this plot. It's got nothing to do with `DESeq2` or any other Bioconductor …
Comment: Limma suqeezeVar by Mengchun • 0
Hi Gordon, Thank you for your reply. I'm working on a proteomics data imputation project, I would like to describe the intensity distribut…
Comment: Heatmap of rnaseq data with z-score scale by giovanna • 0
thank you for your reply. I'm sorry if the question is off topic. the analysis and relative construction of the heatmap was done using bioc…
Answer: Heatmap of rnaseq data with z-score scale by James W. MacDonald 68k
Without including the row names for the heatmap, it's impossible to know if the directionality is switched or not. Do note that the orderin…
Comment: Heatmap of rnaseq data with z-score scale by giovanna • 0
![Figure1][1]![Figure2][2] [1]: /media/images/d62918c5-2886-44ae-930d-91d292c3 [2]: /media/images/421df232-8a9c-4016-bc4a-431ca57a
Votes
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
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