Showing : Normalization • reset
1
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84
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 3 days ago by 66k • written 4 days ago by • 0
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1
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121
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 9 days ago by 42k • written 10 days ago by • 0
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1
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121
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 15 days ago by ★ 4.2k • written 15 days ago by • 0
2
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2
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426
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
6 weeks ago • updated 5 weeks ago Henry ▴ 10
1
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6
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463
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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
0
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2
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201
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
7 weeks ago Marianna ▴ 20
1
vote
4
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328
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
9 weeks ago samuel.channon • 0
0
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0
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178
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
11 weeks ago • updated 9 weeks ago Giovanni Calice ▴ 160
2
votes
1
reply
325
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
2
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2
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450
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
2
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3
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399
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 66k • written 3 months ago by • 0
1
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3
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640
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
339
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 4 months ago by ★ 4.2k • written 4 months ago by • 0
2
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4
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668
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
1
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1
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465
views
DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 4 months ago by 42k • written 4 months ago by • 0
2
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2
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741
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DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
4 months ago Linton • 0
0
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0
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275
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
6 months ago vasily.dobrovolsky • 0
0
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6
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934
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
7 months ago erika.maldonado-rosado • 0
0
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0
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302
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
7 months ago Florian • 0
1
vote
11
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1.1k
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DESeq2 gene length normalisation
Normalization DESeq2
updated 7 months ago by 42k • written 7 months ago by • 0
1
vote
5
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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
0
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3
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624
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Normalization of different input materials
Normalization DESeq2
updated 11 months ago by ★ 4.2k • written 11 months ago by ▴ 10
0
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2
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785
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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
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3.2k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 12 months ago by ▴ 20
0
votes
2
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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
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
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4
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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
0
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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
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
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
1
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6
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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
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 7 months ago by • 0 • written 5.4 years ago by • 0
0
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1
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1.5k
views
EdgeR norm.factor input
Normalization edgeR Normalization edgeR
updated 5 months ago by 50k • written 10.3 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 6 months ago by 50k • written 12.5 years ago by ★ 13k
34 results • Page 1 of 1
Recent ...
Replies
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by Wei Shi ★ 3.6k
Your bam file names should be stored in a vector and then provided to the `files` parameter.
Comment: Volcano plot of scRNA-seq data not "centered" by Michael Love 42k
Agree with @atpoint Depending on the "groups" in single cell, the question of DE can be not well defined without inserting additional inf…
Answer: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
Sounds like a normalization problem, but I am not sure how to help with that. Indeed you can use control genes, for example use the top 20%…
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by ATpoint ★ 4.2k
I was talking about the command line version.
Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by atan • 0
I tried reading in the .csv version of the SAF with header = F and I'm still getting an error. I'm running: ``` counts <- featureCounts( …
Votes
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
Seurat to SingleCellExperiment Converting error in MAC
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