Showing : normalization • reset
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gene detection across experiments
DESeq2 Normalization
10 weeks ago Mara • 0
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3
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1.6k
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RNA-seq: TPM batch effect correction
rnaseqDTU Normalization
updated 10 weeks ago by 68k • written 10 weeks ago by • 0
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5
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694
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WGCNA
WGCNA Normalization RNASeq
written 6 months ago by • 0
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2
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463
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Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis Normalization Epigenetics MethylationArrayData
7 months ago a.alkema • 0
6
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5
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974
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 8 months ago by 68k • written 8 months ago by • 0
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0
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305
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Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization Lipidomics lipidr
9 months ago David R ▴ 90
3
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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
10 months ago dseauer • 0
1
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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
10 months ago Ai • 0
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0
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509
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Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
10 months ago kim • 0
0
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1
reply
849
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 10 months ago by ★ 4.9k • written 10 months ago by • 0
3
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4
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1.1k
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
11 months ago Eva ▴ 10
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0
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517
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Background normalization of Diffbind dba.normalize
Normalization DiffBind
11 months ago Young Boqin • 0
1
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1
reply
518
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 11 months ago by ★ 4.9k • written 11 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 12 months ago by 53k • written 12 months ago by • 0
0
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2
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606
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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
15 months ago Tanvi • 0
2
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2
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797
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 15 months ago by ▴ 10 • written 16 months ago by • 0
0
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2
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900
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
15 months ago sukeshinik5 ▴ 20
0
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1
reply
684
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 16 months ago by 43k • written 16 months ago by • 0
0
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1
reply
662
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 16 months ago by ★ 4.9k • written 16 months ago by • 0
2
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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
17 months ago Henry ▴ 10
1
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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 17 months ago by 43k • written 17 months ago by • 0
0
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2
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857
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
17 months ago Marianna ▴ 20
1
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4
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1.0k
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
18 months ago samuel.channon • 0
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0
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573
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
18 months ago Giovanni Calice ▴ 160
2
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1
reply
729
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 19 months ago by ★ 4.9k • written 19 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
19 months ago jackafiore • 0
2
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3
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1.0k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 19 months ago by 68k • written 19 months ago by • 0
1
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3
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1.2k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 19 months ago by • 0
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1
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1.1k
views
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
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
20 months ago • updated 19 months ago Sabiha ▴ 20
1
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1
reply
978
views
DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 20 months ago by 43k • written 20 months ago by • 0
2
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2
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3.5k
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DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
20 months ago Linton • 0
0
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0
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738
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
22 months ago vasily.dobrovolsky • 0
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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683
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
23 months ago Florian • 0
1
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11
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2.8k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
1
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4
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5.7k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 2.8 years ago by • 0
1
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5
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1.9k
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 2.2 years ago by 53k • written 2.2 years ago by • 0
0
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3
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1.1k
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Normalization of different input materials
Normalization DESeq2
updated 2.2 years ago by ★ 4.9k • written 2.2 years ago by ▴ 10
0
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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
2.3 years ago dwas • 0
5
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11
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7.3k
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Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 2.3 years ago by ▴ 20
0
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3
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1.2k
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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 2.3 years ago by 68k • written 2.3 years ago by • 0
1
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2
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1.6k
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Filter by expression and keep probes in limma
R filter limma Normalization Microarray
2.4 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
1
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2
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969
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 2.4 years ago by • 0
0
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2
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1.5k
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.5 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 2.1 years ago by 53k • written 5.0 years ago by ▴ 20
2
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3
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3.6k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 2.5 years ago by ★ 4.9k • written 2.5 years ago by ▴ 10
2
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1
reply
1.9k
views
deseq2 RLE normalization
RLE normalization deseq2
updated 2.5 years ago by ★ 4.9k • written 2.5 years ago by ▴ 10
1,761 results • Page 1 of 36
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Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Comment: Average biological replicates in RNA-seq by boczniak767 ▴ 740
@atpoint Should I first standardise data and then average replicates?
Comment: 3-factor DESeq2 trime-series analysis by gogeni5529 • 0
Thans you @swbarnes2 for the answer. I can see why trying to include all three parameters might be difficult to interpret. But we're inte…
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Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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