Showing : Normalization • reset
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gene detection across experiments
DESeq2 Normalization
7 months ago Mara • 0
0
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3
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1.9k
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RNA-seq: TPM batch effect correction
rnaseqDTU Normalization
updated 7 months ago by 68k • written 7 months ago by • 0
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5
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1.1k
views
WGCNA
WGCNA Normalization RNASeq
written 11 months ago by • 0
0
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2
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661
views
Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis Normalization Epigenetics MethylationArrayData
12 months ago a.alkema • 0
6
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5
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1.2k
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 13 months ago by 68k • written 13 months ago by • 0
0
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0
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431
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Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization Lipidomics lipidr
14 months ago David R ▴ 90
3
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4
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1.3k
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
15 months ago dseauer • 0
1
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2
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1.5k
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
15 months ago Ai • 0
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0
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784
views
Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
15 months ago kim • 0
0
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1
reply
1.1k
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
7
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4
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1.7k
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
16 months ago Eva ▴ 30
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0
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739
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Background normalization of Diffbind dba.normalize
Normalization DiffBind
16 months ago Young Boqin • 0
1
vote
1
reply
772
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 16 months ago by ★ 5.0k • written 16 months ago by • 0
1
vote
5
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1.8k
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 17 months ago by 53k • written 18 months ago by • 0
0
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2
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758
views
Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 18 months ago by • 0
1
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3
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2.1k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
20 months ago Tanvi • 0
2
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2
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982
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 20 months ago by ▴ 10 • written 21 months ago by • 0
0
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2
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1.1k
views
Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
21 months ago • updated 20 months ago sukeshinik5 ▴ 20
0
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1
reply
867
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 21 months ago by 43k • written 21 months ago by • 0
0
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1
reply
784
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
2
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2
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2.0k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
22 months ago Henry ▴ 10
1
vote
6
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1.9k
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 22 months ago by 43k • written 22 months ago by • 0
0
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2
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1.1k
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
22 months ago Marianna ▴ 20
1
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4
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1.3k
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
23 months ago samuel.channon • 0
0
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0
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657
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
23 months ago Giovanni Calice ▴ 160
2
votes
1
reply
860
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
2
votes
2
replies
1.9k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
2.0 years ago jackafiore • 0
2
votes
3
replies
1.2k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
1
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3
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1.4k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 2.1 years ago by • 0
0
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1
reply
1.3k
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
2
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4
replies
3.0k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
2.1 years ago Sabiha ▴ 20
1
vote
1
reply
1.1k
views
DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
2
votes
2
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4.6k
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
2.1 years ago Linton • 0
0
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0
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933
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
2.2 years ago vasily.dobrovolsky • 0
0
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6
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2.5k
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
2.3 years ago erika.maldonado-rosado • 0
0
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0
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791
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
2.3 years ago Florian • 0
1
vote
11
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3.4k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
1
vote
4
replies
6.4k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 3.2 years ago by • 0
1
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5
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2.1k
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 2.6 years ago by 53k • written 2.6 years ago by • 0
0
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3
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1.2k
views
Normalization of different input materials
Normalization DESeq2
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by ▴ 10
0
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2
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1.7k
views
Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
2.7 years ago dwas • 0
5
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11
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8.2k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 2.7 years ago by ▴ 20
0
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3
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1.4k
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 2.8 years ago by 68k • written 2.8 years ago by • 0
1
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2
replies
1.9k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
2.8 years ago Abdul ▴ 20
2
votes
2
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1.3k
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
2.9 years ago Abdul ▴ 20
1
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2
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1.1k
views
RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 2.9 years ago by • 0
0
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2
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1.8k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.9 years ago Assa Yeroslaviz ★ 1.5k
1
vote
6
replies
3.3k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 2.5 years ago by 53k • written 5.4 years ago by ▴ 20
2
votes
3
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4.0k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by ▴ 10
2
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1
reply
2.1k
views
deseq2 RLE normalization
RLE normalization deseq2
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by ▴ 10
1,761 results • Page 1 of 36
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Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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