Showing : normalization • reset
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
11 days ago vasily.dobrovolsky • 0
0
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6
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354
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
4 weeks ago erika.maldonado-rosado • 0
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129
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
5 weeks ago Florian • 0
1
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11
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542
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 6 weeks ago by 41k • written 6 weeks ago by • 0
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4
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1.2k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 12 months ago by • 0
1
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5
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699
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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 4 months ago by 48k • written 5 months ago by • 0
0
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3
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383
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Normalization of different input materials
Normalization DESeq2
updated 5 months ago by ★ 3.6k • written 5 months ago by ▴ 10
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2
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503
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Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
6 months ago • updated 5 months ago dwas • 0
5
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11
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1.7k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 6 months ago by ▴ 20
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3
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505
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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 6 months ago by 64k • written 6 months ago by • 0
1
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2
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596
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Filter by expression and keep probes in limma
R filter limma Normalization Microarray
7 months ago Abdul ▴ 20
2
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2
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491
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
7 months ago Abdul ▴ 20
1
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2
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424
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 8 months ago by • 0
0
votes
2
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427
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
8 months ago Assa Yeroslaviz ★ 1.5k
1
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6
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1.3k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 3 months ago by 48k • written 3.2 years ago by ▴ 20
2
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3
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1.1k
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deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 8 months ago by ★ 3.6k • written 8 months ago by • 0
1
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1
reply
642
views
deseq2 RLE normalization
RLE normalization deseq2
updated 8 months ago by ★ 3.6k • written 8 months ago by • 0
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1
reply
311
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Using DESeq2 only for normalization
DESeq2 Normalization
updated 8 months ago by ★ 3.6k • written 8 months ago by • 0
0
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1
reply
285
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processing samples with significantly different counts
DESeq2 Normalization
updated 8 months ago by ★ 3.6k • written 8 months ago by • 0
0
votes
5
replies
754
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DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 8 months ago by ★ 3.6k • written 8 months ago by • 0
2
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3
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560
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Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 8 months ago by ★ 3.6k • written 8 months ago by ▴ 20
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1
reply
341
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Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 8 months ago by ★ 3.6k • written 8 months ago by • 0
3
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3
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573
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What is cpmByGroup used for?
edgeR Normalization
updated 9 months ago by 64k • written 9 months ago by • 0
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2
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511
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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
9 months ago rcreswell01 • 0
1
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1
reply
497
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 9 months ago by 48k • written 9 months ago by • 0
4
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2
replies
986
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 9 months ago by ★ 3.6k • written 9 months ago by ▴ 10
0
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1
reply
406
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 10 months ago by 64k • written 10 months ago by • 0
0
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1
reply
854
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How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 10 months ago by 41k • written 10 months ago by ▴ 10
4
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7
replies
1.3k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
10 months ago • updated 9 months ago Bernardo ▴ 10
1
vote
0
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389
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
10 months ago Arend ▴ 10
0
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0
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445
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
10 months ago Zhijie • 0
1
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0
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412
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Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
11 months ago r_grau ▴ 10
3
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4
replies
1.1k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
11 months ago • updated 10 months ago spg • 0
4
votes
8
replies
1.6k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 6 months ago by 48k • written 12 months ago by ▴ 20
0
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1
reply
444
views
TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 12 months ago by ★ 3.6k • written 12 months ago by • 0
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2
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772
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Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 12 months ago by ★ 3.6k • written 12 months ago by • 0
2
votes
4
replies
2.5k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
12 months ago mohammedtoufiq91 ▴ 10
0
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3
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705
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 12 months ago by 48k • written 12 months ago by • 0
0
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2
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555
views
cqn package : Error in if (any(lengths <= 0)) stop("argument 'lengths' need to be greater than zero") : missing value where TRUE/FALSE needed
Normalization R cqn
12 months ago Sally • 0
1
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2
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623
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How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
12 months ago mohammedtoufiq91 ▴ 10
3
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6
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1.4k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
12 months ago Sara • 0
0
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2
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558
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Empty matrix
ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene
13 months ago michela ▴ 20
2
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4
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1.4k
views
Normalizing Cut&Tag peak data
Normalization Peakdata DiffBind Cut&amp;Tag
updated 13 months ago by ★ 3.6k • written 14 months ago by • 0
1
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2
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1.6k
views
Getting the normalized counts after running DESeq()
DESeq2 Normalization
updated 14 months ago by ▴ 10 • written 14 months ago by • 0
0
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1
reply
521
views
Reversing DEseq2 normalization
DESeq2 Normalization RNASeq
updated 14 months ago by 41k • written 15 months ago by • 0
0
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1
reply
512
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DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 15 months ago by 41k • written 15 months ago by • 0
0
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2
replies
5.7k
views
log transform in RMA normalization
Normalization probe Normalization probe
updated 15 months ago by ▴ 20 • written 10.8 years ago by ▴ 440
0
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1
reply
662
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Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile noob Normalization minfi minfiDataEPIC
updated 15 months ago by 64k • written 15 months ago by • 0
1
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1
reply
604
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq Normalization TMM edgeR
updated 16 months ago by 48k • written 16 months ago by ▴ 10
2
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4
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946
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Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
16 months ago Yang Shi ▴ 10
50 results • Page 1 of 1
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Comment: It's possible to use clusterProfiler without an annotationDBI package by nromerov • 0
Thank you very much for your help iu was really deseperate about this that i wasn't thinking too well yesterday im really gratefull with yo…
Comment: Ensembl down??? by bas_work ▴ 20
I want to link 'external_gene_names' (mouse, multiple lists) with the ensembl gene IDs and HGNC symbols of human orthologues using getLDS()…
Answer: SingleR Book Not Found by Peter Hickey ▴ 650
It's not gone, but it also hasn't successfully built since the most recent Bioconductor release ([https://bioconductor.org/checkResults/rel…
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default by James W. MacDonald 64k
The arguments for that function can be found in the help page (accessed using `?DESeqDataSetFromTximport`) ``` Usage: DESeqDataSet(s…
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default by Michael Love 41k
argument txi is missing, with no default This means the function was expecting a named argument txi Check the man page for the funct…
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Answer: gseGO input list
Comment: Problem loading HDF5Array in R 4.3.2
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
Comment: Ensembl down???
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