Showing : normalization • reset
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
22 hours ago • updated 3 hours ago Ai • 0
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0
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31
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Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
1 day ago kim • 0
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1
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247
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 2 days ago by ★ 4.5k • written 3 days ago by • 0
3
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4
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407
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
25 days ago Eva ▴ 10
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0
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108
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Background normalization of Diffbind dba.normalize
Normalization DiffBind
27 days ago Young Boqin • 0
1
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1
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207
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 5 weeks ago by ★ 4.5k • written 5 weeks ago by • 0
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5
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730
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 10 weeks ago by 51k • written 10 weeks ago by • 0
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2
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309
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 11 weeks ago by • 0
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3
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769
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
4 months ago Tanvi • 0
2
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2
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487
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 5 months ago by ▴ 10 • written 5 months ago by • 0
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2
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492
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
5 months ago sukeshinik5 ▴ 20
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1
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359
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 5 months ago by 42k • written 5 months ago by • 0
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1
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343
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 6 months ago by ★ 4.5k • written 6 months ago by • 0
2
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2
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853
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
6 months ago Henry ▴ 10
1
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6
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810
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 7 months ago by 42k • written 7 months ago by • 0
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2
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487
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
7 months ago Marianna ▴ 20
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4
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612
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
7 months ago samuel.channon • 0
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0
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
8 months ago • updated 7 months ago Giovanni Calice ▴ 160
2
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1
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493
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 8 months ago by ★ 4.5k • written 8 months ago by • 0
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2
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932
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
9 months ago jackafiore • 0
2
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3
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644
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 9 months ago by 67k • written 9 months ago by • 0
1
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3
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928
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 9 months ago by • 0
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1
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681
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WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 9 months ago by ★ 4.5k • written 9 months ago by • 0
2
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4
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1.3k
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
9 months ago Sabiha ▴ 20
1
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1
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700
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DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 10 months ago by 42k • written 10 months ago by • 0
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2
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1.7k
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DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
10 months ago Linton • 0
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0
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459
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
11 months ago vasily.dobrovolsky • 0
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6
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1.5k
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
12 months ago erika.maldonado-rosado • 0
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482
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
12 months ago Florian • 0
1
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11
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1.7k
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DESeq2 gene length normalisation
Normalization DESeq2
updated 13 months ago by 42k • written 13 months ago by • 0
1
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4
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3.9k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 23 months ago by • 0
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1.4k
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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 16 months ago by 51k • written 16 months ago by • 0
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3
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Normalization of different input materials
Normalization DESeq2
updated 16 months ago by ★ 4.5k • written 16 months ago by ▴ 10
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1.1k
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Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
17 months ago dwas • 0
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11
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4.7k
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Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 17 months ago by ▴ 20
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3
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965
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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 18 months ago by 67k • written 18 months ago by • 0
1
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2
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1.2k
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Filter by expression and keep probes in limma
R filter limma Normalization Microarray
19 months ago Abdul ▴ 20
2
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2
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871
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
19 months ago Abdul ▴ 20
1
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2
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781
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 19 months ago by • 0
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2
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1.1k
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
19 months ago Assa Yeroslaviz ★ 1.5k
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6
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2.2k
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can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 15 months ago by 51k • written 4.1 years ago by ▴ 20
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3
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2.6k
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deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 19 months ago by ★ 4.5k • written 19 months ago by ▴ 10
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1
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1.4k
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deseq2 RLE normalization
RLE normalization deseq2
updated 19 months ago by ★ 4.5k • written 19 months ago by ▴ 10
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1
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814
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Using DESeq2 only for normalization
DESeq2 Normalization
updated 19 months ago by ★ 4.5k • written 19 months ago by • 0
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1
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574
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processing samples with significantly different counts
DESeq2 Normalization
updated 20 months ago by ★ 4.5k • written 20 months ago by • 0
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5
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1.7k
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DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 19 months ago by ★ 4.5k • written 20 months ago by • 0
2
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3
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1.2k
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Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 19 months ago by ★ 4.5k • written 20 months ago by ▴ 20
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1
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761
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Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 20 months ago by ★ 4.5k • written 20 months ago by • 0
3
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3
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1.0k
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What is cpmByGroup used for?
edgeR Normalization
updated 20 months ago by 67k • written 20 months ago by • 0
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2
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933
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Using Multi-Dimensional Scaling (MDS) to produce a vector in order to account for patient bias when constructing DGE lists from RNA-seq datasets in R?
PrincipalComponent StatisticalMethod edgeR MultidimensionalScaling Normalization
20 months ago rcreswell01 • 0
50 results • Page 1 of 1
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Comment: Consistent Decimals In Data After Antibody Array Background Correction Using Lim by Ai • 0
Hi Gordon, Thank you so much for answering my question and confirming that this is expected! I will go ahead note this down. Sincerely, …
Answer: Annotation for EPICv2 by icecreamlover • 0
Hello, I am also working on analyzing my data from EPICv2 using ChAMP. I used this resource as a guide: https://github.com/YuanTian1991/ChA…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by James W. MacDonald 67k
And it doesn't matter if you're doing gene set analyses after, if the statistics are questionable to begin with.
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by James W. MacDonald 67k
If you're saying that (as an example) you have treated and control in both assay types, and you want to combine and make comparisons betwee…
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Guido Hooiveld ★ 4.1k
I have contacted NCBI, and meanwhile got an an answer. See below. It turns out that the official, HGNC-approved symbols are present in the…
Votes
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
A: How does edgeR cpm function calculate log(CPM) values?
Answer: DecideTest vs topTAGs in edgeR
Comment: DESeq Input from Salmon + tximport/tximeta
Comment: DESeq Input from Salmon + tximport/tximeta
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Popular Question to James W. MacDonald 67k
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