Showing : normalization • reset
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WGCNA
WGCNA Normalization RNASeq
updated 5 weeks ago by • 0 • written 5 weeks ago by • 0
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2
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315
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Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis Normalization Epigenetics MethylationArrayData
7 weeks ago a.alkema • 0
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5
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705
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 11 weeks ago by 68k • written 12 weeks ago by • 0
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197
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Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization Lipidomics lipidr
4 months ago David R ▴ 90
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4
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832
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
4 months ago dseauer • 0
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1.1k
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
4 months ago Ai • 0
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308
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Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
4 months ago kim • 0
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1
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606
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 4 months ago by ★ 4.8k • written 4 months ago by • 0
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4
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794
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
5 months ago Eva ▴ 10
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321
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Background normalization of Diffbind dba.normalize
Normalization DiffBind
5 months ago Young Boqin • 0
1
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1
reply
364
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 6 months ago by ★ 4.8k • written 6 months ago by • 0
1
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5
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1.0k
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 7 months ago by 52k • written 7 months ago by • 0
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2
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456
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 7 months ago by • 0
1
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3
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1.4k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
9 months ago Tanvi • 0
2
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2
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662
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 10 months ago by ▴ 10 • written 10 months ago by • 0
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2
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
10 months ago sukeshinik5 ▴ 20
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1
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511
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 10 months ago by 43k • written 10 months ago by • 0
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1
reply
494
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 10 months ago by ★ 4.8k • written 10 months ago by • 0
2
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2
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1.3k
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
11 months ago Henry ▴ 10
1
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6
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1.2k
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 12 months ago by 43k • written 12 months ago by • 0
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674
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
12 months ago Marianna ▴ 20
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4
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840
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
12 months ago samuel.channon • 0
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475
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
13 months ago • updated 12 months ago Giovanni Calice ▴ 160
2
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1
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 13 months ago by ★ 4.8k • written 13 months ago by • 0
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2
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1.4k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
13 months ago jackafiore • 0
2
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3
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813
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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 14 months ago by • 0
0
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1
reply
900
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 14 months ago by ★ 4.8k • written 14 months ago by • 0
2
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4
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1.7k
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
14 months ago Sabiha ▴ 20
1
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1
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854
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DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 14 months ago by 43k • written 15 months ago by • 0
2
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2
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2.8k
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
15 months ago • updated 14 months ago Linton • 0
0
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598
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
16 months ago vasily.dobrovolsky • 0
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6
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1.9k
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
17 months ago erika.maldonado-rosado • 0
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592
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
17 months ago Florian • 0
1
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11
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2.3k
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DESeq2 gene length normalisation
Normalization DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
1
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4
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4.9k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 2.4 years ago by • 0
1
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5
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1.7k
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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 21 months ago by 52k • written 21 months ago by • 0
0
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3
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952
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Normalization of different input materials
Normalization DESeq2
updated 21 months ago by ★ 4.8k • written 21 months ago by ▴ 10
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2
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1.3k
views
Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
22 months ago dwas • 0
5
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11
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6.2k
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Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 22 months ago by ▴ 20
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3
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1.1k
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 22 months ago by 68k • written 22 months ago by • 0
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2
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1.4k
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Filter by expression and keep probes in limma
R filter limma Normalization Microarray
23 months ago Abdul ▴ 20
2
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2
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991
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
24 months ago Abdul ▴ 20
1
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2
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885
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 24 months ago by • 0
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2
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1.3k
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.0 years ago Assa Yeroslaviz ★ 1.5k
1
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6
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2.6k
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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
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3.2k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 2.0 years ago by ★ 4.8k • written 2.0 years ago by ▴ 10
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1
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1.7k
views
deseq2 RLE normalization
RLE normalization deseq2
updated 2.0 years ago by ★ 4.8k • written 2.0 years ago by ▴ 10
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1
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1.0k
views
Using DESeq2 only for normalization
DESeq2 Normalization
updated 2.0 years ago by ★ 4.8k • written 2.0 years ago by • 0
0
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1
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649
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processing samples with significantly different counts
DESeq2 Normalization
updated 2.0 years ago by ★ 4.8k • written 2.0 years ago by • 0
50 results • Page 1 of 1
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Comment: Design Matrix with paired and independent samples plus RUVg Spike-in normalizati by Mei • 0
I have a similar experiment with 7 paired samples (T0 and T1) in each of 4 outcome groups. I am using RUVr combined with limma-voom, so I a…
Comment: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran by Arctic • 0
Many thanks for the link to the C++ code. I will see if I can find someone with C++ experience to help me with the code breakdown from her…
Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran by Aaron Lun ★ 28k
It's calling C++ code, see the relevant function definitions on [GitHub](https://github.com/knncolle/BiocNeighbors/blob/master/src/generics…
Answer: DESeq2 by ATpoint ★ 4.8k
Time courses are often inevitable batches but you should have done the library prep at the same day, just extract RNA per day. If not then …
Comment: Package developing and interoperation with Bioconductor by slizchap • 0
Thank you so much for your answer. This was very useful, I will optimize my functions so they can handle SE objects.
Votes
Comment: plyranges: find exact GRanges match keeping metadata columns
Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran
Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
Answer: Is it possible to speed up VariantAnnotation's rowRanges function when convertin
Comment: ComBat with repeated measures
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