Showing : normalization • reset
1
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Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 4 hours ago by 47k • written 10 hours ago by • 0
2
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2
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77
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Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 3 days ago by ★ 2.1k • written 3 days ago by ▴ 10
0
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1
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51
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Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 6 days ago by 62k • written 6 days ago by • 0
0
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1
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111
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How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 14 days ago by 39k • written 14 days ago by ▴ 10
3
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6
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182
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How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
updated 3 hours ago by ▴ 40 • written 14 days ago by ▴ 10
1
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0
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88
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Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
26 days ago • updated 24 days ago Arend ▴ 10
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67
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Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
4 weeks ago Zhijie • 0
0
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0
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81
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Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
5 weeks ago r_grau • 0
3
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4
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324
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RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
7 weeks ago • updated 4 weeks ago spg • 0
4
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8
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507
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Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 9 weeks ago by 47k • written 9 weeks ago by ▴ 10
0
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1
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110
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TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 9 weeks ago by ★ 2.1k • written 9 weeks ago by • 0
0
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2
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204
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Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 9 weeks ago by ★ 2.1k • written 10 weeks ago by • 0
2
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4
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386
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Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
9 weeks ago mohammedtoufiq91 ▴ 10
0
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3
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237
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diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 9 weeks ago by 47k • written 10 weeks ago by • 0
1
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2
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177
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
updated 10 weeks ago by • 0 • written 10 weeks ago by • 0
0
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2
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151
views
cqn package : Error in if (any(lengths <= 0)) stop("argument 'lengths' need to be greater than zero") : missing value where TRUE/FALSE needed
Normalization R cqn
11 weeks ago Sally • 0
1
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2
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199
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
11 weeks ago mohammedtoufiq91 ▴ 10
3
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6
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347
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Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
11 weeks ago Sara • 0
0
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2
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189
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Empty matrix
ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene
3 months ago michela ▴ 20
2
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4
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506
views
Normalizing Cut&Tag peak data
Normalization Peakdata DiffBind Cut&amp;Tag
updated 4 months ago by ★ 2.1k • written 4 months ago by • 0
1
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2
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353
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Getting the normalized counts after running DESeq()
DESeq2 Normalization
updated 4 months ago by ▴ 10 • written 4 months ago by • 0
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1
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221
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Reversing DEseq2 normalization
DESeq2 Normalization RNASeq
updated 4 months ago by 39k • written 5 months ago by • 0
0
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1
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198
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DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 5 months ago by 39k • written 5 months ago by • 0
0
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2
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4.8k
views
log transform in RMA normalization
Normalization probe Normalization probe
updated 5 months ago by ▴ 20 • written 10.0 years ago by ▴ 440
0
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1
reply
240
views
Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile noob Normalization minfi minfiDataEPIC
updated 5 months ago by 62k • written 5 months ago by • 0
1
vote
1
reply
239
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq Normalization TMM edgeR
updated 6 months ago by 47k • written 6 months ago by ▴ 10
2
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4
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329
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Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
6 months ago Yang Shi • 0
3
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3
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333
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Log2FoldChange and normalized count values are not consistent?
Normalization DESeq2
8 months ago Karla • 0
0
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0
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188
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Seek for ideas on model-based normalization
Norm Normalization
8 months ago jinghuazhao • 0
2
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7
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663
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CPM after RUVseq
RUVSeq CPM Normalization
8 months ago Jess • 0
3
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3
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452
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Question on RNA-Seq single sample data analysis in EdgeR
R edgeR limma RNASeq Normalization
updated 8 months ago by 47k • written 8 months ago by ▴ 10
0
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1
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422
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after calcNormFactors with EdgeR, how to get TMM normalized matrix?
Normalization edgeR
updated 8 months ago by 47k • written 8 months ago by • 0
2
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3
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393
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DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
9 months ago • updated 8 months ago bers.anthrope • 0
1
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5
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2.5k
views
is it possible to use TPM in DESeq2 ?
counts Normalization DESeq2
updated 9 months ago by ★ 1.2k • written 9 months ago by • 0
1
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1
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301
views
Should I keep libsizes?
Normalization edgeR
updated 9 months ago by 47k • written 9 months ago by • 0
0
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1
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689
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 10 months ago by 39k • written 10 months ago by • 0
0
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1
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1.2k
views
Three questions about processing Agilent Arrays
Normalization limma PROcess Normalization limma PROcess
updated 10 months ago by 47k • written 13.9 years ago by ▴ 30
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0
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197
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Using geNetClassifier with RNA seq data
geNetClassifier Normalization
10 months ago nhaus • 0
1
vote
1
reply
709
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 10 months ago by ▴ 630 • written 10 months ago by • 0
3
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4
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620
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Large difference between naive log2 and rlog transformation of count data
DESeq2 Normalization rlog
updated 10 months ago by 39k • written 10 months ago by • 0
3
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3
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993
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Deseq2 normalization steps
deseq2 normalization
updated 11 months ago by 39k • written 3.7 years ago by • 0
1
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7
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5.0k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray normalization oligo HTA
updated 10 months ago by • 0 • written 4.0 years ago by ▴ 10
2
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5
replies
1.4k
views
DESeq2 median of ratios normalization for signature score calculation
MRN RNASeq Normalization DESeq2
updated 12 months ago by 39k • written 13 months ago by • 0
3
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3
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630
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
written 13 months ago by ▴ 10
0
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1
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480
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small RNA counts
counts SmallRNA Normalization
updated 13 months ago by ▴ 80 • written 15 months ago by ▴ 20
2
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1
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526
views
Converting vst-normalized gene expression counts back after correcting for tumor purity
Inverse-VST Tumor-Purity VST DESeq2 Normalization
updated 14 months ago by 39k • written 14 months ago by • 0
0
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1
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523
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cellHTS2 - normalization with BScore (performance
cellHTS2 Normalization
updated 14 months ago by 13k • written 14 months ago by • 0
0
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9
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941
views
DEseq2 replicate normalization
DEseq2 replicate DESeq2 normalization
14 months ago michael.morash • 0
0
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4
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1.3k
views
Normalization by variance stabilizing transformation VST
library composition vst DESeq2 Normalization
14 months ago kristoffersandas • 0
0
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0
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325
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Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma RNASeq rsem Normalization
15 months ago svlachavas ▴ 800
50 results • Page 1 of 1
Recent ...
Replies
Comment: TCGA: clinical data and expression data by sharifnstu1203002m • 0
Hello, I am in the same problem. I downloaded "transcriptome profiling" data of TCGA by using the Bioconductor package. I get my gene expr…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Jonathan Göke ▴ 40
Great to hear that you are using Bambu. Yes, I think that part of your question does not have one correct answer, there are many ways in wh…
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R by Gordon Smyth 47k
Choosing which samples to normalize together is not dependent on library size but rather on (1) whether the tissue samples are comparable a…
Comment: Atena package - error (new user) by lalanis1 • 0
Thanks a lot, Calvo. Will run my files with revised version soon! Best regards, Lalani
Comment: Nested paired design with covariates in limma by Gordon Smyth 47k
Please post a new question with enough detail to answer your question. If you want bespoke advance, then you need to post the details of yo…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
C: Can't install TopmedPipeline Package
Comment: Question about GWASTools gdsSubset
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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