Showing : normalization • reset
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
3 days ago • updated 21 hours ago sukeshinik5 • 0
1
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1
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105
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 7 days ago by 66k • written 7 days ago by • 0
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1
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128
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 13 days ago by 42k • written 14 days ago by • 0
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1
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126
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 18 days ago by ★ 4.2k • written 18 days ago by • 0
2
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2
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433
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
6 weeks ago Henry ▴ 10
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6
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464
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
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2
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203
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
7 weeks ago Marianna ▴ 20
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4
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331
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
9 weeks ago samuel.channon • 0
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182
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
11 weeks ago • updated 9 weeks ago Giovanni Calice ▴ 160
2
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1
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327
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 3 months ago by ★ 4.2k • written 3 months ago by • 0
2
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2
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454
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
2
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3
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403
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 66k • written 3 months ago by • 0
1
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3
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644
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 4 months ago by • 0
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1
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349
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 4 months ago by ★ 4.2k • written 4 months ago by • 0
2
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4
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671
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
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469
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DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 4 months ago by 42k • written 4 months ago by • 0
2
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2
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754
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DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
4 months ago Linton • 0
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0
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278
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
6 months ago vasily.dobrovolsky • 0
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6
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938
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
7 months ago erika.maldonado-rosado • 0
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305
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
7 months ago Florian • 0
1
vote
11
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1.1k
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DESeq2 gene length normalisation
Normalization DESeq2
updated 7 months ago by 42k • written 7 months ago by • 0
1
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4
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2.8k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 18 months ago by • 0
1
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5
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1.1k
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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 10 months ago by 50k • written 11 months ago by • 0
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3
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Normalization of different input materials
Normalization DESeq2
updated 11 months ago by ★ 4.2k • written 11 months ago by ▴ 10
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2
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792
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Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
12 months ago dwas • 0
5
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11
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3.3k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 12 months ago by ▴ 20
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3
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756
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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 12 months ago by 66k • written 12 months ago by • 0
1
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2
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919
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
13 months ago Abdul ▴ 20
2
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2
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687
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
13 months ago Abdul ▴ 20
1
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2
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629
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 14 months ago by • 0
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2
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774
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
14 months ago Assa Yeroslaviz ★ 1.5k
1
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6
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1.8k
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can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 9 months ago by 50k • written 3.7 years ago by ▴ 20
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3
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1.9k
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deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
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1.0k
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deseq2 RLE normalization
RLE normalization deseq2
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
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1
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569
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Using DESeq2 only for normalization
DESeq2 Normalization
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
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1
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424
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processing samples with significantly different counts
DESeq2 Normalization
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
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5
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1.3k
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DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
2
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3
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946
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Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 14 months ago by ★ 4.2k • written 14 months ago by ▴ 20
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1
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569
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Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
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3
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817
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What is cpmByGroup used for?
edgeR Normalization
updated 15 months ago by 66k • written 15 months ago by • 0
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2
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761
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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
15 months ago rcreswell01 • 0
1
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1
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803
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Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 15 months ago by 50k • written 15 months ago by • 0
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2
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1.8k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 15 months ago by ★ 4.2k • written 15 months ago by ▴ 10
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654
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Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 16 months ago by 66k • written 16 months ago by • 0
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2
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1.6k
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How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 17 days ago by • 0 • written 16 months ago by ▴ 10
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7
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2.1k
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How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
16 months ago • updated 15 months ago Bernardo ▴ 10
1
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0
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591
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
16 months ago Arend ▴ 10
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764
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Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
16 months ago Zhijie • 0
1
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0
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701
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Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
17 months ago r_grau ▴ 10
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4
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1.7k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
17 months ago • updated 16 months ago spg • 0
50 results • Page 1 of 1
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Comment: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)? by ATpoint ★ 4.2k
I don't have an answer to the "why" but maybe a simple reimplemention will do: ```r seqs <- c("ATCATCGTATCAAAGTC", "AAAACGTATCAAAGTC", "TG…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by Guido Hooiveld ★ 4.0k
After checking `?DESeqDataSetFromMatrix` note this information: arguments provided to SummarizedExperiment including rowRanges and met…
Answer: Error in gseDO function by Guido Hooiveld ★ 4.0k
Yes, you are missing something. :-) For a GSEA you will need to use as input all genes that you are analyzing; these genes should be ran…
Comment: GSVA function by Robert Castelo ★ 3.3k
No, negative values may occur after log transformation when the `log(x)` is taken from a positive number `x with 0 < x < 1`, and therefore …
Comment: conumee with Infinium MethylationEPIC v2.0 by sgomez • 0
Hi Max, Could you try this? https://support.bioconductor.org/p/9136138/#9136840
Votes
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
A: DiffBind Batch Effect
A: DiffBind Batch Effect
C: DiffBind Batch Effect
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