Showing : normalization • reset
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gene detection across experiments
DESeq2 Normalization
5 months ago Mara • 0
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3
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1.7k
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RNA-seq: TPM batch effect correction
rnaseqDTU Normalization
updated 5 months ago by 68k • written 5 months ago by • 0
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5
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906
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WGCNA
WGCNA Normalization RNASeq
written 9 months ago by • 0
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2
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541
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Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis Normalization Epigenetics MethylationArrayData
10 months ago a.alkema • 0
6
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5
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1.1k
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 11 months ago by 68k • written 11 months ago by • 0
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0
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378
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Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization Lipidomics lipidr
12 months ago David R ▴ 90
3
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4
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1.2k
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
13 months ago dseauer • 0
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2
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1.4k
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
13 months ago Ai • 0
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0
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609
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Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
13 months ago kim • 0
0
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1
reply
944
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
3
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4
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1.3k
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
14 months ago Eva ▴ 10
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0
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640
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Background normalization of Diffbind dba.normalize
Normalization DiffBind
14 months ago Young Boqin • 0
1
vote
1
reply
710
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
1
vote
5
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1.5k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 15 months ago by 53k • written 16 months ago by • 0
0
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2
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696
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 16 months ago by • 0
1
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3
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1.9k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
18 months ago Tanvi • 0
2
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2
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902
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 18 months ago by ▴ 10 • written 19 months ago by • 0
0
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2
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994
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
19 months ago • updated 18 months ago sukeshinik5 ▴ 20
0
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1
reply
782
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 19 months ago by 43k • written 19 months ago by • 0
0
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1
reply
734
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
2
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2
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1.8k
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
20 months ago Henry ▴ 10
1
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6
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1.7k
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 20 months ago by 43k • written 20 months ago by • 0
0
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2
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956
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
20 months ago Marianna ▴ 20
1
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4
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1.2k
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
21 months ago samuel.channon • 0
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0
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623
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
21 months ago Giovanni Calice ▴ 160
2
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1
reply
807
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
2
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2
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1.7k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
22 months ago jackafiore • 0
2
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3
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1.2k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 22 months ago by 68k • written 22 months ago by • 0
1
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3
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1.3k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 23 months ago by • 0
0
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1
reply
1.2k
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
2
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4
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2.2k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
23 months ago Sabiha ▴ 20
1
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1
reply
1.1k
views
DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 23 months ago by 43k • written 23 months ago by • 0
2
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2
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3.7k
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
23 months ago Linton • 0
0
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0
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825
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
2.1 years ago vasily.dobrovolsky • 0
0
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6
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2.3k
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
2.1 years ago erika.maldonado-rosado • 0
0
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0
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745
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
2.2 years ago Florian • 0
1
vote
11
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3.0k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
1
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4
replies
6.1k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 3.1 years ago by • 0
1
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5
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2.0k
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 2.4 years ago by 53k • written 2.5 years ago by • 0
0
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3
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1.1k
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Normalization of different input materials
Normalization DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by ▴ 10
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2
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1.5k
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Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
2.5 years ago dwas • 0
5
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11
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7.5k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 2.6 years ago by ▴ 20
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3
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1.3k
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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 2.6 years ago by 68k • written 2.6 years ago by • 0
1
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2
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1.8k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
2.7 years ago Abdul ▴ 20
2
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2
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1.2k
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
2.7 years ago Abdul ▴ 20
1
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2
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1.0k
views
RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 2.7 years ago by • 0
0
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2
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1.7k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.7 years ago Assa Yeroslaviz ★ 1.5k
1
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6
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3.1k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 2.4 years ago by 53k • written 5.3 years ago by ▴ 20
2
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3
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3.7k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 10
2
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1
reply
2.0k
views
deseq2 RLE normalization
RLE normalization deseq2
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 10
1,761 results • Page 1 of 36
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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