Showing : normalization • reset
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WGCNA
WGCNA Normalization RNASeq
updated 10 days ago by • 0 • written 11 days ago by • 0
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2
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279
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Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis Normalization Epigenetics MethylationArrayData
26 days ago • updated 25 days ago a.alkema • 0
6
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5
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642
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 7 weeks ago by 68k • written 8 weeks ago by • 0
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0
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180
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Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization Lipidomics lipidr
3 months ago David R ▴ 90
3
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4
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768
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
3 months ago dseauer • 0
1
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2
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1.0k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
3 months ago Ai • 0
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0
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270
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Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
3 months ago kim • 0
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1
reply
523
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 3 months ago by ★ 4.7k • written 4 months ago by • 0
3
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4
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703
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
4 months ago Eva ▴ 10
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0
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271
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Background normalization of Diffbind dba.normalize
Normalization DiffBind
4 months ago Young Boqin • 0
1
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1
reply
326
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 5 months ago by ★ 4.7k • written 5 months ago by • 0
1
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5
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943
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 6 months ago by 52k • written 6 months ago by • 0
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2
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433
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 6 months ago by • 0
1
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3
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1.3k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
8 months ago Tanvi • 0
2
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2
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627
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 9 months ago by ▴ 10 • written 9 months ago by • 0
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2
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652
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
9 months ago sukeshinik5 ▴ 20
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1
reply
481
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 9 months ago by 43k • written 9 months ago by • 0
0
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1
reply
479
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 9 months ago by ★ 4.7k • written 9 months ago by • 0
2
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2
replies
1.2k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
10 months ago Henry ▴ 10
1
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6
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1.1k
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 11 months ago by 43k • written 11 months ago by • 0
0
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2
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639
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
11 months ago Marianna ▴ 20
1
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4
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787
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
11 months ago samuel.channon • 0
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0
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453
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
12 months ago • updated 11 months ago Giovanni Calice ▴ 160
2
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1
reply
581
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 12 months ago by ★ 4.7k • written 12 months ago by • 0
2
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2
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1.2k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
13 months ago • updated 12 months ago jackafiore • 0
2
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3
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774
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 13 months ago by 68k • written 13 months ago by • 0
1
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3
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1.1k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 13 months ago by • 0
0
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1
reply
864
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 13 months ago by ★ 4.7k • written 13 months ago by • 0
2
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4
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1.6k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
13 months ago Sabiha ▴ 20
1
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1
reply
827
views
DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 14 months ago by 43k • written 14 months ago by • 0
2
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2
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2.5k
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
14 months ago Linton • 0
0
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0
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568
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
15 months ago vasily.dobrovolsky • 0
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6
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1.8k
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
16 months ago erika.maldonado-rosado • 0
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0
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572
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
16 months ago Florian • 0
1
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11
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2.2k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
1
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4
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4.7k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 2.3 years ago by • 0
1
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5
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1.6k
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 20 months ago by 52k • written 20 months ago by • 0
0
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3
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928
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Normalization of different input materials
Normalization DESeq2
updated 20 months ago by ★ 4.7k • written 20 months ago by ▴ 10
0
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2
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1.2k
views
Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
21 months ago dwas • 0
5
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11
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5.8k
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Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 21 months ago by ▴ 20
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3
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1.1k
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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 22 months ago by 68k • written 22 months ago by • 0
1
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2
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1.4k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
22 months ago Abdul ▴ 20
2
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2
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969
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
23 months ago Abdul ▴ 20
1
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2
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865
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 23 months ago by • 0
0
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2
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1.2k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
23 months ago Assa Yeroslaviz ★ 1.5k
1
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6
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2.5k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 19 months ago by 52k • written 4.5 years ago by ▴ 20
2
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3
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3.0k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 23 months ago by ★ 4.7k • written 23 months ago by ▴ 10
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1
reply
1.7k
views
deseq2 RLE normalization
RLE normalization deseq2
updated 23 months ago by ★ 4.7k • written 23 months ago by ▴ 10
0
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1
reply
986
views
Using DESeq2 only for normalization
DESeq2 Normalization
updated 23 months ago by ★ 4.7k • written 23 months ago by • 0
0
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1
reply
636
views
processing samples with significantly different counts
DESeq2 Normalization
updated 23 months ago by ★ 4.7k • written 23 months ago by • 0
50 results • Page 1 of 1
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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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