Showing : Normalization • reset
2
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2
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240
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 12 days ago by • 0 • written 26 days ago by • 0
0
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2
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194
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
22 days ago • updated 19 days ago sukeshinik5 • 0
0
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1
reply
155
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
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1
reply
158
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 5 weeks ago by ★ 4.2k • written 5 weeks ago by • 0
2
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2
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462
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
9 weeks ago Henry ▴ 10
1
vote
6
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506
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 10 weeks ago by 42k • written 10 weeks ago by • 0
0
votes
2
replies
236
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
10 weeks ago Marianna ▴ 20
1
vote
4
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352
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
12 weeks ago samuel.channon • 0
0
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0
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201
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
3 months ago • updated 12 weeks ago Giovanni Calice ▴ 160
2
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1
reply
347
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 4 months ago by ★ 4.2k • written 4 months ago by • 0
2
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2
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517
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
4 months ago jackafiore • 0
2
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3
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429
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 4 months ago by 66k • written 4 months ago by • 0
1
vote
3
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667
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 4 months ago by • 0
0
votes
1
reply
397
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 4 months ago by ★ 4.2k • written 4 months ago by • 0
2
votes
4
replies
782
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
1
vote
1
reply
502
views
DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 5 months ago by 42k • written 5 months ago by • 0
2
votes
2
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845
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
5 months ago Linton • 0
0
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0
replies
295
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
7 months ago vasily.dobrovolsky • 0
0
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6
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1.0k
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
7 months ago erika.maldonado-rosado • 0
0
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0
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317
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
8 months ago Florian • 0
1
vote
11
replies
1.2k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 8 months ago by 42k • written 8 months ago by • 0
1
vote
4
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2.9k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 19 months ago by • 0
1
vote
5
replies
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 11 months ago by 51k • written 11 months ago by • 0
0
votes
3
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650
views
Normalization of different input materials
Normalization DESeq2
updated 11 months ago by ★ 4.2k • written 11 months ago by ▴ 10
0
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2
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827
views
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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3.4k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 12 months ago by ▴ 20
0
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3
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775
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq normalization PCR_efficiency bias intrasample_comparison
updated 13 months ago by 66k • written 13 months ago by • 0
1
vote
2
replies
962
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
14 months ago Abdul ▴ 20
2
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2
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705
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
14 months ago Abdul ▴ 20
1
vote
2
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644
views
RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 14 months ago by • 0
0
votes
2
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810
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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
vote
6
replies
1.9k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 10 months ago by 51k • written 3.8 years ago by ▴ 20
2
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3
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2.0k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
1
vote
1
reply
1.1k
views
deseq2 RLE normalization
RLE normalization deseq2
updated 15 months ago by ★ 4.2k • written 15 months ago by • 0
0
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1
reply
590
views
Using DESeq2 only for normalization
DESeq2 Normalization
updated 15 months ago by ★ 4.2k • written 15 months ago by • 0
0
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1
reply
437
views
processing samples with significantly different counts
DESeq2 Normalization
updated 15 months ago by ★ 4.2k • written 15 months ago by • 0
0
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5
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1.3k
views
DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 15 months ago by ★ 4.2k • written 15 months ago by • 0
2
votes
3
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986
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 14 months ago by ★ 4.2k • written 15 months ago by ▴ 20
0
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1
reply
592
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 15 months ago by ★ 4.2k • written 15 months ago by • 0
3
votes
3
replies
840
views
What is cpmByGroup used for?
edgeR Normalization
updated 16 months ago by 66k • written 16 months ago by • 0
0
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2
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776
views
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
16 months ago rcreswell01 • 0
1
vote
1
reply
828
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 16 months ago by 51k • written 16 months ago by • 0
4
votes
2
replies
1.9k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 16 months ago by ★ 4.2k • written 16 months ago by ▴ 10
0
votes
1
reply
675
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 16 months ago by 66k • written 16 months ago by • 0
0
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2
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1.6k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 5 weeks ago by • 0 • written 16 months ago by ▴ 10
4
votes
7
replies
2.2k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
16 months ago Bernardo ▴ 10
1
vote
0
replies
606
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
17 months ago Arend ▴ 10
0
votes
0
replies
790
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
17 months ago Zhijie • 0
1
vote
0
replies
727
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
17 months ago r_grau ▴ 10
3
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4
replies
1.8k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
18 months ago • updated 17 months ago spg • 0
50 results • Page 1 of 1
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Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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