Showing : normalization • reset
2
votes
2
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389
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
24 days ago • updated 23 days ago Henry ▴ 10
1
vote
6
replies
434
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
0
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2
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170
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
4 weeks ago Marianna ▴ 20
1
vote
4
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295
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
6 weeks ago samuel.channon • 0
0
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0
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152
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
8 weeks ago • updated 6 weeks ago Giovanni Calice ▴ 160
6
votes
11
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4.0k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 7 weeks ago by • 0 • written 3.2 years ago by ▴ 40
2
votes
1
reply
303
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 11 weeks ago by ★ 4.1k • written 11 weeks ago by • 0
2
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2
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410
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
12 weeks ago jackafiore • 0
2
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3
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371
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
1
vote
3
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581
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 3 months ago by • 0
0
votes
1
reply
301
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
2
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4
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593
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
1
vote
1
reply
417
views
DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 3 months ago by 41k • written 4 months ago by • 0
2
votes
2
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638
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
4 months ago Linton • 0
0
votes
1
reply
1.5k
views
EdgeR norm.factor input
Normalization edgeR Normalization edgeR
updated 4 months ago by 50k • written 10.2 years ago by ★ 13k
4
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4
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2.1k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 5 months ago by 50k • written 2.4 years ago by ▴ 10
0
votes
0
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251
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
5 months ago vasily.dobrovolsky • 0
0
votes
3
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2.5k
views
Background correction with neqc
Normalization Cancer Normalization Cancer
updated 6 months ago by 50k • written 12.4 years ago by ★ 13k
0
votes
6
replies
860
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
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 5.4 years ago by • 0
0
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0
replies
283
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
1
vote
11
replies
1.0k
views
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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2.6k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 17 months ago by • 0
0
votes
2
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2.3k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 8 months ago by • 0 • written 2.1 years ago by • 0
1
vote
6
replies
1.8k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 9 months ago by 50k • written 3.6 years ago by ▴ 20
1
vote
5
replies
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 10 months ago by 50k • written 10 months ago by • 0
0
votes
3
replies
612
views
Normalization of different input materials
Normalization DESeq2
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
0
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2
replies
757
views
Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
11 months ago dwas • 0
5
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11
replies
3.0k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 11 months ago by ▴ 20
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 11 months ago by 50k • written 17 months ago by ▴ 20
0
votes
3
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714
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 12 months ago by 65k • written 12 months ago by • 0
1
vote
2
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901
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
12 months ago Abdul ▴ 20
2
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2
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668
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
13 months ago Abdul ▴ 20
2
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6
replies
2.5k
views
RNA-seq analysis across different experiments
limma deseq2 normalization degenes design and contrast matrix
written 6.8 years ago by ▴ 10
1
vote
2
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621
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 13 months ago by • 0
0
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2
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717
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
13 months ago Assa Yeroslaviz ★ 1.5k
2
votes
3
replies
1.8k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
2
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3
replies
894
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 13 months ago by ★ 4.1k • written 14 months ago by ▴ 20
9
votes
10
replies
6.8k
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 13 months ago by • 0 • written 3.5 years ago by ▴ 10
0
votes
5
replies
1.2k
views
DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
1
vote
1
reply
994
views
deseq2 RLE normalization
RLE normalization deseq2
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
votes
1
reply
547
views
Using DESeq2 only for normalization
DESeq2 Normalization
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
votes
1
reply
413
views
processing samples with significantly different counts
DESeq2 Normalization
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
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2
replies
1.0k
views
best way to normalize for differences in sample read depth: normalize genome vs cn.MOPs
cn.mops normalization
updated 13 months ago by • 0 • written 6.1 years ago by • 0
0
votes
1
reply
541
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
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2
replies
738
views
Using Multi-Dimensional Scaling (MDS) to produce a vector in order to account for patient bias when constructing DGE lists from RNA-seq datasets in R?
PrincipalComponent StatisticalMethod edgeR MultidimensionalScaling Normalization
14 months ago rcreswell01 • 0
3
votes
3
replies
804
views
What is cpmByGroup used for?
edgeR Normalization
updated 14 months ago by 65k • written 14 months ago by • 0
4
votes
7
replies
2.0k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
15 months ago Bernardo ▴ 10
1
vote
1
reply
772
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 15 months ago by 50k • written 15 months ago by • 0
4
votes
2
replies
1.7k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 15 months ago by ★ 4.1k • written 15 months ago by ▴ 10
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Answer: How to save the DEXSeq results by Michael Love 41k
If you look at the output here: https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#4_Testing_for_differe…
Answer: Method to find pathways different between 2 groups by Robert Castelo ★ 3.3k
Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package …
Answer: Couldn't connect to server while using "pathways" by James W. MacDonald 65k
As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide eno…
Answer: Trim/Filter out-of-bounds GRanges by Michael Love 41k
https://support.bioconductor.org/p/73432/#73448
Comment: Couldn't connect to server while using "pathways" by Michael Love 41k
You've put the tag "DESeq2" which results in an email to the maintainer, me, that I should respond to a post on the support site. Can you …
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Answer: Method to find pathways different between 2 groups
Answer: Method to find pathways different between 2 groups
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
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