Showing : normalization • reset
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 6 days ago by ★ 4.5k • written 6 days ago by • 0
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5
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675
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 6 weeks ago by 51k • written 6 weeks ago by • 0
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2
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273
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 6 weeks ago by • 0
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3
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655
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
3 months ago Tanvi • 0
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2
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455
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 4 months ago by ▴ 10 • written 4 months ago by • 0
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2
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456
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
4 months ago sukeshinik5 • 0
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1
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325
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 4 months ago by 42k • written 4 months ago by • 0
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1
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304
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 5 months ago by ★ 4.5k • written 5 months ago by • 0
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2
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759
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
5 months ago Henry ▴ 10
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6
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775
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 6 months ago by 42k • written 6 months ago by • 0
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2
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444
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 months ago Marianna ▴ 20
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4
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565
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
6 months ago samuel.channon • 0
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0
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
7 months ago • updated 6 months ago Giovanni Calice ▴ 160
2
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1
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463
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 7 months ago by ★ 4.5k • written 7 months ago by • 0
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2
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846
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
8 months ago jackafiore • 0
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3
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 8 months ago by 67k • written 8 months ago by • 0
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3
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895
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 8 months ago by • 0
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1
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642
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WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 8 months ago by ★ 4.5k • written 8 months ago by • 0
2
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4
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1.2k
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
8 months ago Sabiha ▴ 20
1
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1
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674
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DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 9 months ago by 42k • written 9 months ago by • 0
2
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2
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1.5k
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DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
9 months ago Linton • 0
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434
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
10 months ago vasily.dobrovolsky • 0
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1.4k
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
11 months ago erika.maldonado-rosado • 0
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459
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
11 months ago Florian • 0
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11
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1.6k
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DESeq2 gene length normalisation
Normalization DESeq2
updated 12 months ago by 42k • written 12 months ago by • 0
1
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4
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3.7k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 22 months ago by • 0
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5
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1.4k
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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 15 months ago by 51k • written 15 months ago by • 0
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3
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789
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Normalization of different input materials
Normalization DESeq2
updated 15 months ago by ★ 4.5k • written 15 months ago by ▴ 10
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2
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1.0k
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Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
16 months ago dwas • 0
5
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11
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4.4k
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Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 16 months ago by ▴ 20
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3
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942
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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 17 months ago by 67k • written 17 months ago by • 0
1
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2
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1.1k
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Filter by expression and keep probes in limma
R filter limma Normalization Microarray
18 months ago Abdul ▴ 20
2
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2
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832
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
18 months ago Abdul ▴ 20
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2
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765
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 18 months ago by • 0
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2
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1.0k
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
18 months ago Assa Yeroslaviz ★ 1.5k
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6
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2.2k
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can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 14 months ago by 51k • written 4.1 years ago by ▴ 20
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3
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2.5k
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deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 18 months ago by ★ 4.5k • written 18 months ago by • 0
1
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1
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1.3k
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deseq2 RLE normalization
RLE normalization deseq2
updated 18 months ago by ★ 4.5k • written 18 months ago by • 0
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1
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771
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Using DESeq2 only for normalization
DESeq2 Normalization
updated 18 months ago by ★ 4.5k • written 18 months ago by • 0
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1
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545
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processing samples with significantly different counts
DESeq2 Normalization
updated 19 months ago by ★ 4.5k • written 19 months ago by • 0
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5
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1.6k
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DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 18 months ago by ★ 4.5k • written 19 months ago by • 0
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3
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1.2k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 18 months ago by ★ 4.5k • written 19 months ago by ▴ 20
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1
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726
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Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 19 months ago by ★ 4.5k • written 19 months ago by • 0
3
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3
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978
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What is cpmByGroup used for?
edgeR Normalization
updated 19 months ago by 67k • written 19 months ago by • 0
0
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2
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907
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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
19 months ago rcreswell01 • 0
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976
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Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 20 months ago by 51k • written 20 months ago by • 0
6
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2
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2.5k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 20 months ago by ★ 4.5k • written 20 months ago by ▴ 10
0
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1
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804
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Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 20 months ago by 67k • written 20 months ago by • 0
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2
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2.0k
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How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 5 months ago by • 0 • written 20 months ago by ▴ 10
4
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8
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2.9k
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How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
updated 11 weeks ago by • 0 • written 20 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: heatmap with batch effect by James W. MacDonald 67k
When you use `removeBatchEffect` it is simply computing the mean expression for each group and subtracting that out. If you have variabilit…
Comment: Highly DE genes but small count difference within conditions by bioshot.com • 0
These are the MA plot for design=~sex+genotype and boxplots with `boxplot(log10(counts(dds)+1))` ![MA plot][1] ![sample_boxplot][2] ![box][…
Comment: miRTarRnaseq library by María Calvo • 0
Hello, Im using "Part3- Identify significant miRNA mRNA relationships for 2 time points from fold changes". In mRNA data and miRNA data, th…
Comment: heatmap with batch effect by tothuhien • 0
Hi, thank you very much for your reply. Yes what you said is true. Sorry I forgot to say that this is a just subset of samples. There are m…
Comment: Highly DE genes but small count difference within conditions by Michael Love 42k
TPM is not a robust scaling method and can be influenced by changes in global distribution. What do you get with an MA plot. Can you high…
Votes
GSVA ssGSEA vs. Broad implementation of ssGSEA
Answer: How to control batch effect if Group and batch are same?
Answer: How to control batch effect if Group and batch are same?
Answer: How to control batch effect if Group and batch are same?
Comment: Convert HGVS Representation back to Reference Genome Coordinates
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