Showing : Normalization • reset
5
votes
10
replies
361
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
updated 2 days ago by 47k • written 4 days ago by ▴ 20
0
votes
3
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197
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq normalization PCR_efficiency bias intrasample_comparison
updated 20 days ago by 63k • written 20 days ago by • 0
1
vote
2
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201
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Filter by expression and keep probes in limma
R filter limma Normalization Microarray
6 weeks ago Abdul ▴ 20
2
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2
replies
266
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
7 weeks ago Abdul ▴ 20
1
vote
2
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182
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 8 weeks ago by • 0
0
votes
2
replies
130
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
8 weeks ago Assa Yeroslaviz ★ 1.5k
1
vote
4
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804
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
2.7 years ago • updated 8 weeks ago linouhao ▴ 20
2
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3
replies
311
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 9 weeks ago by ★ 2.9k • written 9 weeks ago by • 0
1
vote
1
reply
214
views
deseq2 RLE normalization
RLE normalization deseq2
updated 10 weeks ago by ★ 2.9k • written 10 weeks ago by • 0
0
votes
1
reply
127
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Using DESeq2 only for normalization
DESeq2 Normalization
updated 10 weeks ago by ★ 2.9k • written 10 weeks ago by • 0
0
votes
1
reply
118
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processing samples with significantly different counts
DESeq2 Normalization
updated 10 weeks ago by ★ 2.9k • written 11 weeks ago by • 0
0
votes
5
replies
342
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DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 10 weeks ago by ★ 2.9k • written 11 weeks ago by • 0
1
vote
3
replies
199
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 9 weeks ago by ★ 2.9k • written 11 weeks ago by • 0
0
votes
1
reply
131
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 11 weeks ago by ★ 2.9k • written 11 weeks ago by • 0
3
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3
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261
views
What is cpmByGroup used for?
edgeR Normalization
updated 3 months ago by 63k • written 3 months ago by • 0
0
votes
2
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207
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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
3 months ago rcreswell01 • 0
1
vote
1
reply
216
views
Library sizes of miRNA sequencing data and TMM normalization with Edge-R
edgeR SequencingData miRNA TMM Normalization
updated 3 months ago by 47k • written 3 months ago by • 0
4
votes
2
replies
333
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 3 months ago by ★ 2.9k • written 3 months ago by ▴ 10
0
votes
1
reply
160
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 4 months ago by 63k • written 4 months ago by • 0
0
votes
1
reply
358
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 4 months ago by 40k • written 4 months ago by ▴ 10
4
votes
7
replies
579
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
4 months ago • updated 3 months ago Bernardo ▴ 10
1
vote
0
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174
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
4 months ago Arend ▴ 10
0
votes
0
replies
172
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
4 months ago Zhijie • 0
1
vote
0
replies
209
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
5 months ago r_grau ▴ 10
3
votes
4
replies
580
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
5 months ago • updated 4 months ago spg • 0
4
votes
8
replies
849
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 4 days ago by 47k • written 5 months ago by ▴ 20
0
votes
1
reply
224
views
TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 6 months ago by ★ 2.9k • written 6 months ago by • 0
0
votes
2
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420
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Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 6 months ago by ★ 2.9k • written 6 months ago by • 0
2
votes
4
replies
1.2k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
6 months ago mohammedtoufiq91 ▴ 10
0
votes
3
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412
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 6 months ago by 47k • written 6 months ago by • 0
1
vote
3
replies
361
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
updated 6 weeks ago by • 0 • written 6 months ago by • 0
0
votes
2
replies
271
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
6 months ago Sally • 0
1
vote
2
replies
333
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
6 months ago mohammedtoufiq91 ▴ 10
3
votes
6
replies
690
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
6 months ago Sara • 0
0
votes
2
replies
296
views
Empty matrix
ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene
7 months ago michela ▴ 20
2
votes
4
replies
819
views
Normalizing Cut&Tag peak data
Normalization Peakdata DiffBind Cut&amp;Tag
updated 7 months ago by ★ 2.9k • written 7 months ago by • 0
1
vote
2
replies
752
views
Getting the normalized counts after running DESeq()
DESeq2 Normalization
updated 8 months ago by ▴ 10 • written 8 months ago by • 0
0
votes
1
reply
333
views
Reversing DEseq2 normalization
DESeq2 Normalization RNASeq
updated 8 months ago by 40k • written 9 months ago by • 0
0
votes
1
reply
301
views
DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 9 months ago by 40k • written 9 months ago by • 0
0
votes
2
replies
5.2k
views
log transform in RMA normalization
Normalization probe Normalization probe
updated 9 months ago by ▴ 20 • written 10.4 years ago by ▴ 440
0
votes
1
reply
385
views
Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile noob Normalization minfi minfiDataEPIC
updated 9 months ago by 63k • written 9 months ago by • 0
1
vote
1
reply
349
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq Normalization TMM edgeR
updated 10 months ago by 47k • written 10 months ago by ▴ 10
2
votes
4
replies
515
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
10 months ago Yang Shi ▴ 10
3
votes
3
replies
496
views
Log2FoldChange and normalized count values are not consistent?
Normalization DESeq2
11 months ago Karla • 0
0
votes
0
replies
271
views
Seek for ideas on model-based normalization
Norm Normalization
12 months ago jinghuazhao • 0
2
votes
7
replies
854
views
CPM after RUVseq
RUVSeq CPM Normalization
12 months ago Jess • 0
3
votes
3
replies
696
views
Question on RNA-Seq single sample data analysis in EdgeR
R edgeR limma RNASeq Normalization
updated 12 months ago by 47k • written 12 months ago by ▴ 10
0
votes
1
reply
553
views
after calcNormFactors with EdgeR, how to get TMM normalized matrix?
Normalization edgeR
updated 12 months ago by 47k • written 12 months ago by • 0
2
votes
3
replies
522
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
13 months ago • updated 12 months ago bers.anthrope • 0
1
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5
replies
4.0k
views
is it possible to use TPM in DESeq2 ?
counts Normalization DESeq2
updated 12 months ago by ★ 1.2k • written 12 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10
@gordonsmyth thank you, yes, please find the targets frame below. Basically, I want to create a design matrix and binarize by 0 and 1 to be…
Comment: WGCNA: many over and under-expressed features in modules of a signed network by andres.firrincieli ▴ 50
answered in Biostars: https://www.biostars.org/p/9564943/
Comment: Multitasking and Rbwa by Jean-Philippe Fortin • 0
Indeed, one can pass additional arguments to the `bwa_aln` function in `Rbwa`: bwa_aln(type="single", index_prefix=index_pr…
Comment: biomaRt error: database disk image is malformed by Emile • 0
UNBORKING the bioMaRt cache `biomaRt::biomartCacheClear()` also fixes the troubles with PANTHER.db installation which have also something t…
Answer: Proteomics data with NA values by Laurent Gatto 1.6k
- First, you need to assess how many missing values you have. - I would recommend not to impute your data by 0 (or any arbitrary small …
Votes
Answer: Question on constructing design matrix and defining contrasts for analysis
WGCNA: many over and under-expressed features in modules of a signed network
Comment: WGCNA: many over and under-expressed features in modules of a signed network
Answer: DESeq2 or edgeR for Presence and Absence of Proteins
Answer: Normalized counts from LRT or Wald test?
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