Showing : normalization • reset
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
6 days ago • updated 5 days ago Henry ▴ 10
1
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6
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388
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 14 days ago by 41k • written 14 days ago by • 0
0
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2
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134
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
14 days ago Marianna ▴ 20
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4
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240
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
28 days ago samuel.channon • 0
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0
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
6 weeks ago • updated 29 days ago Giovanni Calice ▴ 160
2
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1
reply
272
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 8 weeks ago by ★ 4.0k • written 9 weeks ago by • 0
2
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2
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355
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
10 weeks ago jackafiore • 0
2
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3
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327
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
1
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3
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539
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 11 weeks ago by • 0
0
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1
reply
255
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WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 12 weeks ago by ★ 4.0k • written 12 weeks ago by • 0
2
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4
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
12 weeks ago Sabiha ▴ 20
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vote
1
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377
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DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 3 months ago by 41k • written 3 months ago by • 0
2
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2
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544
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DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
3 months ago Linton • 0
0
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0
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
5 months ago vasily.dobrovolsky • 0
0
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6
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789
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
5 months ago erika.maldonado-rosado • 0
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255
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
1
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11
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962
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DESeq2 gene length normalisation
Normalization DESeq2
updated 6 months ago by 41k • written 6 months ago by • 0
1
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4
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2.4k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 17 months ago by • 0
1
vote
5
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993
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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 9 months ago by 50k • written 9 months ago by • 0
0
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3
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Normalization of different input materials
Normalization DESeq2
updated 9 months ago by ★ 4.0k • written 9 months ago by ▴ 10
0
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2
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723
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Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
10 months ago dwas • 0
5
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11
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2.9k
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Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 10 months ago by ▴ 20
0
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3
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688
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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 11 months ago by 65k • written 11 months ago by • 0
1
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6
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1.7k
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can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 8 months ago by 50k • written 3.6 years ago by ▴ 20
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8
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2.1k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 10 months ago by 50k • written 16 months ago by ▴ 20
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2
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2.2k
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Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 7 months ago by • 0 • written 2.0 years ago by • 0
4
votes
4
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2.0k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 4 months ago by 50k • written 2.3 years ago by ▴ 10
6
votes
11
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3.9k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 5 weeks ago by • 0 • written 3.1 years ago by ▴ 40
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 6 months ago by • 0 • written 5.3 years ago by • 0
0
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1
reply
1.4k
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EdgeR norm.factor input
Normalization edgeR Normalization edgeR
updated 4 months ago by 50k • written 10.2 years ago by ★ 13k
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3
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2.5k
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Background correction with neqc
Normalization Cancer Normalization Cancer
updated 5 months ago by 50k • written 12.4 years ago by ★ 13k
31 results • Page 1 of 1
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Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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