Showing : normalization • reset
2
votes
2
replies
389
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
24 days ago • updated 23 days ago Henry ▴ 10
1
vote
6
replies
434
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
0
votes
2
replies
169
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
4 weeks ago Marianna ▴ 20
1
vote
4
replies
295
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
6 weeks ago samuel.channon • 0
0
votes
0
replies
152
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
8 weeks ago • updated 6 weeks ago Giovanni Calice ▴ 160
2
votes
1
reply
302
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 11 weeks ago by ★ 4.1k • written 11 weeks ago by • 0
2
votes
2
replies
410
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
12 weeks ago jackafiore • 0
2
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3
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371
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
1
vote
3
replies
581
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 3 months ago by • 0
0
votes
1
reply
299
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
2
votes
4
replies
590
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
1
vote
1
reply
417
views
DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 3 months ago by 41k • written 4 months ago by • 0
2
votes
2
replies
638
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
4 months ago Linton • 0
0
votes
0
replies
251
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
5 months ago vasily.dobrovolsky • 0
0
votes
6
replies
859
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
0
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0
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283
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
1
vote
11
replies
1.0k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 6 months ago by 41k • written 6 months ago by • 0
1
vote
5
replies
1.0k
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
votes
3
replies
612
views
Normalization of different input materials
Normalization DESeq2
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
0
votes
2
replies
757
views
Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
11 months ago dwas • 0
5
votes
11
replies
3.0k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 11 months ago by ▴ 20
0
votes
3
replies
713
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 12 months ago by 65k • written 12 months ago by • 0
1
vote
2
replies
901
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
12 months ago Abdul ▴ 20
2
votes
2
replies
668
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
13 months ago Abdul ▴ 20
1
vote
2
replies
621
views
RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 13 months ago by • 0
0
votes
2
replies
717
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
13 months ago Assa Yeroslaviz ★ 1.5k
2
votes
3
replies
1.8k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
votes
1
reply
547
views
Using DESeq2 only for normalization
DESeq2 Normalization
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
1
vote
1
reply
994
views
deseq2 RLE normalization
RLE normalization deseq2
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
votes
5
replies
1.2k
views
DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
votes
1
reply
413
views
processing samples with significantly different counts
DESeq2 Normalization
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
2
votes
3
replies
894
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 13 months ago by ★ 4.1k • written 13 months ago by ▴ 20
0
votes
1
reply
541
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
3
votes
3
replies
804
views
What is cpmByGroup used for?
edgeR Normalization
updated 14 months ago by 65k • written 14 months ago by • 0
0
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2
replies
738
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
14 months ago rcreswell01 • 0
1
vote
1
reply
772
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 15 months ago by 50k • written 15 months ago by • 0
4
votes
2
replies
1.7k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 15 months ago by ★ 4.1k • written 15 months ago by ▴ 10
0
votes
1
reply
634
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 15 months ago by 65k • written 15 months ago by • 0
4
votes
7
replies
2.0k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
15 months ago Bernardo ▴ 10
0
votes
1
reply
1.3k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 15 months ago by 41k • written 15 months ago by ▴ 10
1
vote
0
replies
577
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
16 months ago • updated 15 months ago Arend ▴ 10
0
votes
0
replies
736
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
16 months ago Zhijie • 0
1
vote
0
replies
674
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
16 months ago r_grau ▴ 10
3
votes
4
replies
1.6k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
16 months ago spg • 0
4
votes
8
replies
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
0
votes
1
reply
633
views
TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 17 months ago by ★ 4.1k • written 17 months ago by • 0
2
votes
4
replies
3.5k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
17 months ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
997
views
Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 17 months ago by ★ 4.1k • written 17 months ago by • 0
0
votes
3
replies
954
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 17 months ago by 50k • written 17 months ago by • 0
1
vote
4
replies
2.6k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 17 months ago by • 0
50 results • Page 1 of 1
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Comment: Couldn't connect to server while using "pathways" by Michael Love 41k
You've put the tag "DESeq2" which results in an email to the maintainer, me, that I should respond to a post on the support site. Can you …
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Vincent J. Carey, Jr. 6.7k
btw that was run on M1 mac
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Vincent J. Carey, Jr. 6.7k
the test is not portable > aa <- aa_mutmat(acc = "MIYS930101", aaindex = "aaindex2") > str(aa) num [1:20, 1:20] 0.34 -0.0…
Comment: Method to find pathways different between 2 groups by Chris • 0
Sorry for not clear. I just try to find papers use this method for learning purpose. So I may know when to use this method. This paper comp…
Comment: Improving the design matrices vignette in RNAseq123 by Lluís Revilla Sancho ▴ 730
Cool. Thanks for looking into it.
Votes
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
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