Showing : Normalization • reset
5
votes
11
replies
3.2k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 12 months ago by ▴ 20
1
vote
11
replies
1.1k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 7 months ago by 42k • written 7 months ago by • 0
6
votes
11
replies
4.1k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 10 weeks ago by • 0 • written 3.2 years ago by ▴ 40
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 12 months ago by 50k • written 17 months ago by ▴ 20
1
vote
6
replies
463
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 7 weeks ago by 42k • written 7 weeks 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 3.7 years ago by ▴ 20
0
votes
6
replies
931
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
7 months ago • updated 6 months ago erika.maldonado-rosado • 0
1
vote
5
replies
1.1k
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
2
votes
5
replies
11k
views
Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 7 months ago by • 0 • written 5.4 years ago by • 0
1
vote
4
replies
325
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
9 weeks ago samuel.channon • 0
2
votes
4
replies
665
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
1
vote
4
replies
2.7k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 18 months ago by • 0
4
votes
4
replies
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
3
replies
624
views
Normalization of different input materials
Normalization DESeq2
updated 10 months ago by ★ 4.2k • written 11 months ago by ▴ 10
2
votes
3
replies
398
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 66k • written 3 months ago by • 0
1
vote
3
replies
638
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 3 months ago by • 0
0
votes
3
replies
2.5k
views
Background correction with neqc
Normalization Cancer Normalization Cancer
updated 6 months ago by 50k • written 12.5 years ago by ★ 13k
2
votes
2
replies
448
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
2
votes
2
replies
740
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
4 months ago Linton • 0
2
votes
2
replies
424
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
5 weeks ago Henry ▴ 10
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 13 days ago by • 0 • written 16 months ago by ▴ 10
0
votes
2
replies
785
views
Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
11 months ago dwas • 0
0
votes
2
replies
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
0
votes
2
replies
201
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
7 weeks ago Marianna ▴ 20
0
votes
1
reply
120
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 14 days ago by ★ 4.2k • written 14 days ago by • 0
0
votes
1
reply
1.5k
views
EdgeR norm.factor input
Normalization edgeR Normalization edgeR
updated 5 months ago by 50k • written 10.3 years ago by ★ 13k
1
vote
1
reply
76
views
Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 2 days ago by 66k • written 3 days ago by • 0
1
vote
1
reply
461
views
DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 4 months ago by 42k • written 4 months ago by • 0
0
votes
1
reply
339
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 4 months ago by ★ 4.2k • written 4 months ago by • 0
0
votes
1
reply
117
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 8 days ago by 42k • written 9 days ago by • 0
2
votes
1
reply
322
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 3 months ago by ★ 4.2k • written 3 months ago by • 0
0
votes
0
replies
177
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
11 weeks ago • updated 9 weeks ago Giovanni Calice ▴ 160
0
votes
0
replies
273
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
6 months ago vasily.dobrovolsky • 0
0
votes
0
replies
301
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
7 months ago Florian • 0
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I solved the problem installing the latest R version (4.4.0)
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Answer: Get gene symbols for a set of hg19 coordinates
Answer: Get gene symbols for a set of hg19 coordinates
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