Showing : Normalization • reset
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 7 hours ago by 65k • written 13 hours ago by • 0
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104
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 6 days ago by 42k • written 7 days ago by • 0
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2
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1.5k
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How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 10 days ago by • 0 • written 16 months ago by ▴ 10
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1
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115
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 11 days ago by ★ 4.1k • written 11 days ago by • 0
2
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2
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420
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
5 weeks ago Henry ▴ 10
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6
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460
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
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2
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199
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 weeks ago Marianna ▴ 20
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4
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317
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
8 weeks ago samuel.channon • 0
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172
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
10 weeks ago • updated 8 weeks ago Giovanni Calice ▴ 160
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11
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views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 10 weeks ago by • 0 • written 3.2 years ago by ▴ 40
2
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321
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
2
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2
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441
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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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392
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
1
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3
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630
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 3 months ago by • 0
0
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1
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336
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
2
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4
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653
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago • updated 3 months ago Sabiha ▴ 20
1
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1
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453
views
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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718
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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
0
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1
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1.5k
views
EdgeR norm.factor input
Normalization edgeR Normalization edgeR
updated 5 months ago by 50k • written 10.3 years ago by ★ 13k
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4
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2.1k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 5 months ago by 50k • written 2.4 years ago by ▴ 10
0
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268
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
6 months ago vasily.dobrovolsky • 0
0
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3
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2.5k
views
Background correction with neqc
Normalization Cancer Normalization Cancer
updated 6 months ago by 50k • written 12.5 years ago by ★ 13k
0
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6
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926
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
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5
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11k
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Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 7 months ago by • 0 • written 5.4 years ago by • 0
0
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0
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300
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
7 months ago Florian • 0
1
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11
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1.1k
views
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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2.7k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 18 months ago by • 0
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2
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2.3k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 8 months ago by • 0 • written 2.1 years ago by • 0
1
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6
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1.8k
views
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
1
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5
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1.1k
views
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 10 months ago by • 0
0
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3
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621
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Normalization of different input materials
Normalization DESeq2
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
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2
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782
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Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
11 months ago dwas • 0
5
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11
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3.2k
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Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 11 months ago by ▴ 20
4
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8
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2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 11 months ago by 50k • written 17 months ago by ▴ 20
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3
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740
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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 65k • written 12 months ago by • 0
1
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2
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915
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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684
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
13 months ago Abdul ▴ 20
2
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6
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2.5k
views
RNA-seq analysis across different experiments
limma deseq2 normalization degenes design and contrast matrix
written 6.8 years ago by ▴ 10
1
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2
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625
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 13 months ago by • 0
0
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2
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755
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
13 months ago Assa Yeroslaviz ★ 1.5k
2
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3
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1.9k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 13 months ago by ★ 4.1k • written 14 months ago by • 0
2
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3
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932
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 14 months ago by ★ 4.1k • written 14 months ago by ▴ 20
9
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10
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6.9k
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 14 months ago by ▴ 10 • written 3.6 years ago by ▴ 10
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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 ★ 4.1k • written 14 months ago by • 0
1
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1
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1.0k
views
deseq2 RLE normalization
RLE normalization deseq2
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
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1
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562
views
Using DESeq2 only for normalization
DESeq2 Normalization
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
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1
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421
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processing samples with significantly different counts
DESeq2 Normalization
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
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2
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1.0k
views
best way to normalize for differences in sample read depth: normalize genome vs cn.MOPs
cn.mops normalization
updated 14 months ago by • 0 • written 6.2 years ago by • 0
0
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1
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560
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
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2
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755
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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
50 results • Page 1 of 1
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Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 65k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 65k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat by minardsmitha ▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons by boczniak767 ▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
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Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
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