Showing : Normalization • reset
2
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351
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
13 days ago • updated 12 days ago Henry ▴ 10
1
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6
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401
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 20 days ago by 41k • written 21 days ago by • 0
0
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2
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144
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
21 days ago Marianna ▴ 20
1
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4
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263
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
5 weeks ago • updated 4 weeks ago samuel.channon • 0
0
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0
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136
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
7 weeks ago • updated 5 weeks ago Giovanni Calice ▴ 160
2
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1
reply
279
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 9 weeks ago by ★ 4.0k • written 10 weeks ago by • 0
2
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2
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375
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
11 weeks ago jackafiore • 0
2
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3
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350
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
1
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3
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552
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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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268
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
2
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4
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542
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
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1
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393
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DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 3 months ago by 41k • written 3 months ago by • 0
2
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2
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581
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DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
3 months ago Linton • 0
0
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0
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238
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
5 months ago vasily.dobrovolsky • 0
0
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6
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806
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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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263
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
1
vote
11
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986
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DESeq2 gene length normalisation
Normalization DESeq2
updated 6 months ago by 41k • written 6 months ago by • 0
1
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4
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2.5k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 17 months ago by • 0
1
vote
5
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1.0k
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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 9 months ago by 50k • written 9 months ago by • 0
0
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3
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Normalization of different input materials
Normalization DESeq2
updated 10 months ago by ★ 4.0k • written 10 months ago by ▴ 10
0
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2
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732
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Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
10 months ago dwas • 0
5
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11
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2.9k
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Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 11 months ago by ▴ 20
0
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3
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700
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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 11 months ago by 65k • written 11 months ago by • 0
1
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2
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868
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Filter by expression and keep probes in limma
R filter limma Normalization Microarray
12 months ago Abdul ▴ 20
2
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2
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648
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
12 months ago Abdul ▴ 20
1
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2
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606
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 12 months ago by • 0
0
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2
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697
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
13 months ago Assa Yeroslaviz ★ 1.5k
1
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6
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1.7k
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can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 8 months ago by 50k • written 3.6 years ago by ▴ 20
2
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3
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1.8k
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deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
1
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1
reply
965
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deseq2 RLE normalization
RLE normalization deseq2
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
0
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1
reply
532
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Using DESeq2 only for normalization
DESeq2 Normalization
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
0
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1
reply
403
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processing samples with significantly different counts
DESeq2 Normalization
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
0
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5
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1.2k
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DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
2
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3
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870
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Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 13 months ago by ★ 4.0k • written 13 months ago by ▴ 20
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1
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528
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Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
3
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3
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785
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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
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721
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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
14 months ago rcreswell01 • 0
1
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1
reply
747
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Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 14 months ago by 50k • written 14 months ago by • 0
4
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2
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1.7k
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Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 14 months ago by ★ 4.0k • written 14 months ago by ▴ 10
0
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1
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622
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Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 14 months ago by 65k • written 14 months ago by • 0
0
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1
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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
4
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7
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2.0k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
15 months ago • updated 14 months ago Bernardo ▴ 10
1
vote
0
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564
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
15 months ago Arend ▴ 10
0
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0
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715
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Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
15 months ago Zhijie • 0
1
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0
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648
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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
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4
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1.6k
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RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
16 months ago • updated 15 months ago spg • 0
4
votes
8
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2.1k
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 16 months ago by ▴ 20
0
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1
reply
619
views
TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 17 months ago by ★ 4.0k • written 17 months ago by • 0
0
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2
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970
views
Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 17 months ago by ★ 4.0k • written 17 months ago by • 0
2
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4
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3.4k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
17 months ago mohammedtoufiq91 ▴ 10
50 results • Page 1 of 1
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Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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