Showing : normalization • reset
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small RNA counts
counts SmallRNA Normalization
updated 3.9 years ago by ▴ 80 • written 4.0 years ago by ▴ 30
2
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1
reply
1.7k
views
Converting vst-normalized gene expression counts back after correcting for tumor purity
Inverse-VST Tumor-Purity VST DESeq2 Normalization
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
0
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1
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1.4k
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cellHTS2 - normalization with BScore (performance
cellHTS2 Normalization
updated 3.9 years ago by ★ 13k • written 3.9 years ago by • 0
0
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9
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2.4k
views
DEseq2 replicate normalization
DEseq2 replicate DESeq2 normalization
3.9 years ago michael.morash • 0
0
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4
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5.1k
views
Normalization by variance stabilizing transformation VST
library composition vst DESeq2 Normalization
4.0 years ago kristoffersandas • 0
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0
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1.0k
views
Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma RNASeq rsem Normalization
4.0 years ago svlachavas ▴ 840
4
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6
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2.0k
views
RMA on different disease labels
rma background microarray normalization
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
3
votes
2
replies
1.5k
views
DESeq2 normalization when using with derfinder
Normalization DESeq2 derfinder
4.0 years ago Debayan ▴ 20
0
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1
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1.5k
views
Question about normalizing and removing batch effects from bulk RNA-seq data from NCBI-SRA
Arabidopsis_thaliana_Data RNASeqR Normalization BatchEffect
updated 4.1 years ago by 68k • written 4.1 years ago by ▴ 20
7
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12
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6.2k
views
.fastq to .txt conversion for EdgeR package and merging two paired end sequence files
EdgeR normalization fastq txt TMM
updated 3.5 years ago by 53k • written 10.0 years ago by • 0
0
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0
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1.4k
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DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
4.1 years ago Drew • 0
1
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1
reply
1.4k
views
Degust: what normalization method does it use
DEGUST Normalization CPM
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
0
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4
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1.3k
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Clarify some basic concepts about DESeq normalization
deseq2 rnaseq normalization
written 7.7 years ago by • 0
2
votes
2
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1.7k
views
Normalizing 5' Nascent RNA-seq data to identify differentially expressed transcription start sites
DESeq2 tpm Normalization
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
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2
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1.8k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
4.3 years ago maria.soler • 0
2
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3
replies
2.0k
views
vst of DESeq2 for bulk UMI counts
DESeq2 normaliz Normalization
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
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1
reply
1.6k
views
Re-normalize microarray dataset in R
microarray quantile expression R Normalization
updated 4.3 years ago by ▴ 90 • written 4.3 years ago by ▴ 10
0
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1
reply
1.4k
views
DESseq2 question about VST and rlog
DESeq2 Normalization
updated 4.4 years ago by ★ 5.0k • written 4.4 years ago by • 0
1
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0
replies
2.4k
views
Normalization of metabolomics/lipidomics data for limma
Lipidomics Metabolomics limma Normalization
4.4 years ago pgugger ▴ 70
1
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1
reply
1.2k
views
DiffBind normalisation factor retrieval
edgeR Normalization DiffBind
updated 4.4 years ago by ★ 5.2k • written 4.4 years ago by • 0
0
votes
5
replies
1.8k
views
Tximport/DESeq2 Normalization Process
tximport Normalization DESeq2
updated 4.4 years ago by 43k • written 4.5 years ago by • 0
1
vote
1
reply
2.4k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 4.4 years ago by ★ 1.1k • written 4.5 years ago by ▴ 20
2
votes
2
replies
1.5k
views
Subscript out of bounds while normalising using affy::rma()
Normalization affy AffymetrixChip
4.5 years ago geoffrey ▴ 10
0
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4
replies
1.6k
views
subtracting or normalizing RNAseq reads when samples have contaminating reads
Normalization RNASeq contamination edgeR DESeq2
4.5 years ago Yuqia • 0
0
votes
0
replies
969
views
Cross-cultivar RNA-seq analysis
RNA Normalization
4.6 years ago nancy • 0
1
vote
12
replies
3.1k
views
Data normalization
DESeq2 Normalization
4.6 years ago nolwenn • 0
0
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1
reply
999
views
DESEQ2 normalization for time series data
DESeq2 Normalization Medianofratios
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
3
votes
3
replies
1.9k
views
Weird MAplot with DEGs lying along the diagonals
limma Microarray AgilentChip MA-plot Normalization
4.7 years ago FedeXandeR • 0
6
votes
11
replies
6.5k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 20 months ago by • 0 • written 4.7 years ago by ▴ 40
0
votes
1
reply
3.2k
views
How to plot the RMA log2 normalised data from Affymetrix
log2 RMA Affymetrix affy Normalization
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by • 0
2
votes
2
replies
1.6k
views
Preprocessing Issue
sva RNASeq Preprocessing Normalization BatchEffect
updated 4.7 years ago by ★ 5.0k • written 4.7 years ago by • 0
0
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0
replies
1.2k
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
4.8 years ago wrzl • 0
1
vote
3
replies
2.8k
views
Normalization for two bulk RNA datasets with different library sizes
Normalization BulkRNA-seq DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
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1
reply
1.1k
views
error using cqn package
Normalization cqn
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 30
2
votes
2
replies
843
views
Normalisation in DESeq2
DESeq2 Normalization
5.0 years ago • updated 4.9 years ago Bine ▴ 50
1
vote
2
replies
1.5k
views
Analyzing publicly available DESeq2 normalized counts for differential expression
DifferentialExpression DESeq2 Normalization
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
2
votes
3
replies
3.0k
views
Normalization for within-sample gene correlation
edgeR Normalization DESeq2 tpm RNASeq
updated 5.0 years ago by 53k • written 5.0 years ago by ▴ 100
0
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2
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1.4k
views
extract certain subpopulation of MouseGastrulationData
MouseGastrulationData Normalization BatchEffect
updated 5.0 years ago by ▴ 90 • written 5.0 years ago by ▴ 120
0
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3
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1.3k
views
Is it possible in DiffBind to specify sizeFactors for DESeq2 analysis?
diffbind normalization
updated 5.0 years ago by ★ 5.2k • written 9.4 years ago by • 0
1
vote
4
replies
2.6k
views
MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 5.0 years ago by ★ 5.2k • written 7.8 years ago by • 0
0
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1
reply
1.5k
views
Normalisation of protein micro array data using VSN
microarray normalization protein
updated 5.0 years ago by ★ 13k • written 6.4 years ago by • 0
0
votes
10
replies
2.7k
views
Do I have clustering by library size?
PCA DESeq2 Normalization librarysize
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 10
1
vote
9
replies
4.7k
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 3.0 years ago by ▴ 670 • written 5.0 years ago by ▴ 10
1
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1
reply
2.2k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 5.0 years ago by ★ 5.2k
9
votes
10
replies
9.6k
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 2.7 years ago by ▴ 20 • written 5.1 years ago by ▴ 10
1
vote
5
replies
1.3k
views
DESeq2 Normalization causing overcorrection in libaries sizes for a few samples
deseq2 normalization
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
2
votes
7
replies
3.6k
views
EdgeR diffSpliceDGE: Obtaining exon-level counts and normalisation step
edger normalization differential exon usage splicing
updated 5.1 years ago by ▴ 900 • written 5.1 years ago by • 0
1
vote
5
replies
2.0k
views
DESeq2 library composition adjustment in size factors
deseq2 normalization
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
1
vote
5
replies
1.4k
views
technical replicates and normalization/log transformation
deseq2 normalization
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 60
1
vote
2
replies
1.2k
views
tcga and geo train and validation sets
deseq2 normalization
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 20
1,761 results • Page 3 of 36
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Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated by RalphSavage99 • 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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