Showing : normalization • reset
6
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5
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550
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 21 days ago by 67k • written 27 days ago by • 0
0
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0
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152
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Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization Lipidomics lipidr
9 weeks ago David R ▴ 90
3
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4
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680
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
10 weeks ago dseauer • 0
1
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2
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982
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
12 weeks ago Ai • 0
0
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0
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225
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Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
12 weeks ago kim • 0
0
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1
reply
424
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 12 weeks ago by ★ 4.6k • written 12 weeks ago by • 0
3
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4
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620
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
3 months ago Eva ▴ 10
0
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0
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220
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Background normalization of Diffbind dba.normalize
Normalization DiffBind
3 months ago Young Boqin • 0
1
vote
1
reply
285
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 3 months ago by ★ 4.6k • written 3 months ago by • 0
1
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5
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880
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 5 months ago by 52k • written 5 months ago by • 0
0
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2
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391
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 5 months ago by • 0
1
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3
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1.1k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
7 months ago Tanvi • 0
2
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2
replies
585
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 7 months ago by ▴ 10 • written 8 months ago by • 0
0
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2
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603
views
Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
8 months ago sukeshinik5 ▴ 20
0
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1
reply
447
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 8 months ago by 43k • written 8 months ago by • 0
0
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1
reply
430
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 8 months ago by ★ 4.6k • written 8 months ago by • 0
2
votes
2
replies
1.1k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
9 months ago Henry ▴ 10
1
vote
6
replies
992
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 10 months ago by 43k • written 10 months ago by • 0
0
votes
2
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600
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
10 months ago Marianna ▴ 20
1
vote
4
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734
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
10 months ago samuel.channon • 0
0
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0
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430
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
10 months ago Giovanni Calice ▴ 160
2
votes
1
reply
552
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 11 months ago by ★ 4.6k • written 11 months ago by • 0
2
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2
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1.1k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
11 months ago jackafiore • 0
2
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3
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733
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 months ago by 67k • written 11 months ago by • 0
1
vote
3
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1.0k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 12 months ago by • 0
0
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1
reply
806
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 12 months ago by ★ 4.6k • written 12 months ago by • 0
2
votes
4
replies
1.5k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
12 months ago Sabiha ▴ 20
1
vote
1
reply
781
views
DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 12 months ago by 43k • written 12 months ago by • 0
2
votes
2
replies
2.2k
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
12 months ago Linton • 0
0
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0
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531
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
14 months ago vasily.dobrovolsky • 0
0
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6
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1.7k
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
15 months ago erika.maldonado-rosado • 0
0
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0
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541
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
15 months ago Florian • 0
1
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11
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2.0k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
1
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4
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4.5k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 2.2 years ago by • 0
1
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5
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1.5k
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 19 months ago by 52k • written 19 months ago by • 0
0
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3
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893
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Normalization of different input materials
Normalization DESeq2
updated 19 months ago by ★ 4.6k • written 19 months ago by ▴ 10
0
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2
replies
1.2k
views
Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
20 months ago dwas • 0
5
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11
replies
5.5k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 20 months ago by ▴ 20
0
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3
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1.0k
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 20 months ago by 67k • written 20 months ago by • 0
1
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2
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1.3k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
21 months ago Abdul ▴ 20
2
votes
2
replies
924
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
22 months ago Abdul ▴ 20
1
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2
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840
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 22 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
22 months ago Assa Yeroslaviz ★ 1.5k
1
vote
6
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2.4k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 17 months ago by 52k • written 4.4 years ago by ▴ 20
2
votes
3
replies
2.9k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 22 months ago by ★ 4.6k • written 22 months ago by ▴ 10
2
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1
reply
1.6k
views
deseq2 RLE normalization
RLE normalization deseq2
updated 22 months ago by ★ 4.6k • written 22 months ago by ▴ 10
0
votes
1
reply
926
views
Using DESeq2 only for normalization
DESeq2 Normalization
updated 22 months ago by ★ 4.6k • written 22 months ago by • 0
0
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1
reply
615
views
processing samples with significantly different counts
DESeq2 Normalization
updated 22 months ago by ★ 4.6k • written 22 months ago by • 0
0
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5
replies
1.8k
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DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 22 months ago by ★ 4.6k • written 22 months ago by • 0
2
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3
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1.4k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 22 months ago by ★ 4.6k • written 22 months ago by ▴ 20
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
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