Showing : Normalization • reset
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Using DESeq2 only for normalization
DESeq2 Normalization
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
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processing samples with significantly different counts
DESeq2 Normalization
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
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5
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2.3k
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DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
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3
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1.8k
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Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 20
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Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
3
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3
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What is cpmByGroup used for?
edgeR Normalization
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
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2
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1.4k
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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
2.8 years ago rcreswell01 • 0
1
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1.3k
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Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
6
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Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 10
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Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
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How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 19 months ago by • 0 • written 2.9 years ago by ▴ 10
4
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How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
updated 16 months ago by • 0 • written 2.9 years ago by ▴ 10
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Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
2.9 years ago Arend ▴ 10
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1.4k
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Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
2.9 years ago Zhijie • 0
1
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1.3k
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Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
2.9 years ago r_grau ▴ 10
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4
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3.1k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
3.0 years ago • updated 2.9 years ago spg • 0
4
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8
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Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 2.5 years ago by 53k • written 3.0 years ago by ▴ 20
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TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
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2
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Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
2
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4
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Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
3.0 years ago mohammedtoufiq91 ▴ 10
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3
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1.8k
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
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2
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1.3k
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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
3.0 years ago Sally • 0
1
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2
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1.4k
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
3.0 years ago mohammedtoufiq91 ▴ 10
3
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6
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3.4k
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Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
3.0 years ago Sara • 0
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2
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1.2k
views
Empty matrix
ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene
3.1 years ago michela ▴ 20
2
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4
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3.8k
views
Normalizing Cut&Tag peak data
Normalization Peakdata DiffBind Cut&amp;Tag
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by ▴ 20
1
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2
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5.3k
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Getting the normalized counts after running DESeq()
DESeq2 Normalization
updated 3.2 years ago by ▴ 10 • written 3.2 years ago by • 0
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932
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Reversing DEseq2 normalization
DESeq2 Normalization RNASeq
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
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5
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2.4k
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DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 6 months ago by 43k • written 3.3 years ago by • 0
2
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2
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7.8k
views
log transform in RMA normalization
Normalization probe Normalization probe
updated 3.3 years ago by ▴ 200 • written 12.9 years ago by ▴ 450
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1
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1.8k
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Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile noob Normalization minfi minfiDataEPIC
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
1
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1
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1.4k
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Filtering Orthologus Genes Before or After TMM normalization?
RNASeq Normalization TMM edgeR
updated 3.3 years ago by 53k • written 3.3 years ago by ▴ 10
2
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4
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2.7k
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Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
3.4 years ago Yang Shi ▴ 10
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3
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3.1k
views
Log2FoldChange and normalized count values are not consistent?
Normalization DESeq2
3.5 years ago Karla ▴ 10
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622
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Seek for ideas on model-based normalization
Norm Normalization
3.5 years ago jinghuazhao • 0
2
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7
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2.4k
views
CPM after RUVseq
RUVSeq CPM Normalization
3.5 years ago Jess • 0
3
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3
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2.5k
views
Question on RNA-Seq single sample data analysis in EdgeR
R edgeR limma RNASeq Normalization
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 10
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2.0k
views
after calcNormFactors with EdgeR, how to get TMM normalized matrix?
Normalization edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
2
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3
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1.6k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
3.6 years ago • updated 3.5 years ago bers.anthrope ▴ 10
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5
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13k
views
is it possible to use TPM in DESeq2 ?
counts Normalization DESeq2
updated 3.6 years ago by ★ 1.4k • written 3.6 years ago by ▴ 10
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1
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1.3k
views
Should I keep libsizes?
Normalization edgeR
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
0
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2
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4.1k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 2.3 years ago by • 0 • written 3.6 years ago by • 0
0
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1
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2.0k
views
Three questions about processing Agilent Arrays
Normalization limma PROcess Normalization limma PROcess
updated 3.7 years ago by 53k • written 16.8 years ago by ▴ 30
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0
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898
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Using geNetClassifier with RNA seq data
geNetClassifier Normalization
3.7 years ago nhaus ▴ 70
1
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1
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2.9k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 3.7 years ago by ▴ 760 • written 3.7 years ago by • 0
3
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4
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2.5k
views
Large difference between naive log2 and rlog transformation of count data
DESeq2 Normalization rlog
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
3
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3
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2.4k
views
Deseq2 normalization steps
deseq2 normalization
updated 3.8 years ago by 43k • written 6.5 years ago by • 0
1
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7
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10k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray normalization oligo HTA
updated 3.7 years ago by • 0 • written 6.9 years ago by ▴ 10
3
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5
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4.7k
views
DESeq2 median of ratios normalization for signature score calculation
MRN RNASeq Normalization DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 10
4
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4
replies
3.5k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 2.0 years ago by 53k • written 4.0 years ago by ▴ 10
1,761 results • Page 2 of 36
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Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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