Showing : normalization • reset
2
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
8 days ago • updated 7 days ago Henry ▴ 10
1
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6
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393
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 16 days ago by 41k • written 16 days ago by • 0
0
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2
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141
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
17 days ago • updated 16 days ago Marianna ▴ 20
1
vote
4
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253
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
4 weeks ago samuel.channon • 0
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 4 weeks ago Giovanni Calice ▴ 160
2
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1
reply
276
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 9 weeks ago by ★ 4.0k • written 9 weeks ago by • 0
2
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2
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363
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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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336
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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
vote
3
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543
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 12 weeks ago by • 0
0
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1
reply
257
views
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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525
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago • updated 12 weeks ago Sabiha ▴ 20
1
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1
reply
382
views
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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560
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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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799
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
5 months ago erika.maldonado-rosado • 0
0
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258
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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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971
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DESeq2 gene length normalisation
Normalization DESeq2
updated 6 months ago by 41k • written 6 months ago by • 0
1
vote
4
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2.4k
views
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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1.0k
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 9 months ago by 50k • written 9 months ago by • 0
0
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3
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588
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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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726
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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
votes
11
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2.9k
views
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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692
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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
views
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
4
votes
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
0
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2
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2.2k
views
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
replies
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
replies
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
votes
5
replies
11k
views
Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 6 months ago by • 0 • written 5.4 years ago by • 0
0
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1
reply
1.4k
views
EdgeR norm.factor input
Normalization edgeR Normalization edgeR
updated 4 months ago by 50k • written 10.2 years ago by ★ 13k
0
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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: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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