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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749
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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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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 2.8 years ago by ★ 5.0k • written 2.8 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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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 2.9 years ago by 68k • written 2.9 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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8
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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
1
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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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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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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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1
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1.2k
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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
1
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3
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1.8k
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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
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
3.1 years ago • updated 3.0 years ago Sally • 0
1
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2
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1.5k
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
3.1 years ago mohammedtoufiq91 ▴ 10
3
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6
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3.5k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
3.1 years ago • updated 3.0 years ago Sara • 0
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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5.4k
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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
0
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1
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933
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Reversing DEseq2 normalization
DESeq2 Normalization RNASeq
updated 3.2 years ago by 43k • written 3.3 years ago by • 0
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 3.4 years ago by 53k • written 3.4 years ago by ▴ 10
2
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4
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2.7k
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
3.4 years ago Yang Shi ▴ 10
4
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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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626
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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
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CPM after RUVseq
RUVSeq CPM Normalization
3.6 years ago • updated 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 3.6 years ago by ▴ 10
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2.0k
views
after calcNormFactors with EdgeR, how to get TMM normalized matrix?
Normalization edgeR
updated 3.6 years ago by 53k • written 3.6 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
1
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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
1
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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 3.7 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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901
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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 6.6 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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4.8k
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
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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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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
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…
Votes
C: DESeq2 Following RSEM
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
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