Showing : normalization • reset
2
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2
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351
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
13 days ago • updated 12 days ago Henry ▴ 10
1
vote
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
vote
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
6
votes
11
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3.9k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 6 weeks ago by • 0 • written 3.2 years ago by ▴ 40
2
votes
1
reply
279
views
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
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
reply
269
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
replies
543
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
394
views
DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 3 months ago by 41k • written 3 months ago by • 0
2
votes
2
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582
views
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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1
reply
1.4k
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EdgeR norm.factor input
Normalization edgeR Normalization edgeR
updated 4 months ago by 50k • written 10.2 years ago by ★ 13k
4
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4
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2.0k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 4 months ago by 50k • written 2.4 years ago by ▴ 10
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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3
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2.5k
views
Background correction with neqc
Normalization Cancer Normalization Cancer
updated 5 months ago by 50k • written 12.4 years ago by ★ 13k
0
votes
6
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806
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
2
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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 6 months ago by • 0 • written 5.4 years ago by • 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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988
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 6 months ago by 41k • written 6 months ago by • 0
1
vote
4
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2.5k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 17 months ago by • 0
0
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2
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2.2k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 7 months ago by • 0 • written 2.0 years ago by • 0
1
vote
6
replies
1.7k
views
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
1
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5
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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 9 months ago by 50k • written 9 months ago by • 0
0
votes
3
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594
views
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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733
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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
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 11 months ago by ▴ 20
4
votes
8
replies
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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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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869
views
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
2
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6
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2.4k
views
RNA-seq analysis across different experiments
limma deseq2 normalization degenes design and contrast matrix
written 6.7 years ago by ▴ 10
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
2
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3
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1.8k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
2
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3
replies
870
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 13 months ago by ★ 4.0k • written 13 months ago by ▴ 20
9
votes
10
replies
6.8k
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 13 months ago by • 0 • written 3.5 years ago by ▴ 10
0
votes
5
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1.2k
views
DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
1
vote
1
reply
965
views
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
views
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
views
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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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 13 months ago by • 0 • written 6.1 years ago by • 0
0
votes
1
reply
529
views
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
0
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2
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721
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
3
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3
replies
785
views
What is cpmByGroup used for?
edgeR Normalization
updated 14 months ago by 65k • written 14 months ago by • 0
4
votes
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
1
reply
747
views
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
views
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
50 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
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.
Answer: 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…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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