Showing : Normalization • reset
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Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization Lipidomics lipidr
12 days ago David R ▴ 90
3
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4
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579
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
24 days ago • updated 23 days ago dseauer • 0
1
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2
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913
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
4 weeks ago Ai • 0
0
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0
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135
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Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
4 weeks ago kim • 0
0
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1
reply
350
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 4 weeks ago by ★ 4.6k • written 5 weeks ago by • 0
3
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4
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484
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
8 weeks ago Eva ▴ 10
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0
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150
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Background normalization of Diffbind dba.normalize
Normalization DiffBind
8 weeks ago Young Boqin • 0
1
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1
reply
239
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
1
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5
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814
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 3 months ago by 52k • written 3 months ago by • 0
0
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2
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343
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 3 months ago by • 0
1
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3
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896
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
5 months ago Tanvi • 0
2
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2
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524
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 6 months ago by ▴ 10 • written 6 months ago by • 0
0
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2
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537
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
6 months ago sukeshinik5 ▴ 20
0
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1
reply
393
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 6 months ago by 43k • written 6 months ago by • 0
0
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1
reply
384
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 7 months ago by ★ 4.6k • written 7 months ago by • 0
2
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2
replies
938
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
8 months ago • updated 7 months ago Henry ▴ 10
1
vote
6
replies
851
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 8 months ago by 43k • written 8 months ago by • 0
0
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2
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529
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
8 months ago Marianna ▴ 20
1
vote
4
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668
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
8 months ago samuel.channon • 0
0
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0
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385
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
9 months ago • updated 8 months ago Giovanni Calice ▴ 160
2
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1
reply
517
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 9 months ago by ★ 4.6k • written 9 months ago by • 0
2
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2
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1.0k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
10 months ago jackafiore • 0
2
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3
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677
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 10 months ago by 67k • written 10 months ago by • 0
1
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3
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976
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 10 months ago by • 0
0
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1
reply
720
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 10 months ago by ★ 4.6k • written 10 months ago by • 0
2
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4
replies
1.4k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
10 months ago Sabiha ▴ 20
1
vote
1
reply
726
views
DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 11 months ago by 43k • written 11 months ago by • 0
2
votes
2
replies
1.9k
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
11 months ago Linton • 0
0
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0
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488
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
12 months ago vasily.dobrovolsky • 0
0
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6
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1.6k
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
13 months ago erika.maldonado-rosado • 0
0
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0
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504
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
13 months ago Florian • 0
1
vote
11
replies
1.9k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
1
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4
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4.1k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 2.0 years ago by • 0
1
vote
5
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1.5k
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 17 months ago by 52k • written 17 months ago by • 0
0
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3
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854
views
Normalization of different input materials
Normalization DESeq2
updated 17 months ago by ★ 4.6k • written 17 months ago by ▴ 10
0
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2
replies
1.1k
views
Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
18 months ago dwas • 0
5
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11
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5.0k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 18 months ago by ▴ 20
0
votes
3
replies
988
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 19 months ago by 67k • written 19 months ago by • 0
1
vote
2
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1.2k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
20 months ago Abdul ▴ 20
2
votes
2
replies
889
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
20 months ago Abdul ▴ 20
1
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2
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802
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 20 months ago by • 0
0
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2
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1.1k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
20 months ago Assa Yeroslaviz ★ 1.5k
1
vote
6
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2.3k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 16 months ago by 52k • written 4.2 years ago by ▴ 20
2
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3
replies
2.7k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 20 months ago by ★ 4.6k • written 20 months ago by ▴ 10
2
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1
reply
1.5k
views
deseq2 RLE normalization
RLE normalization deseq2
updated 21 months ago by ★ 4.6k • written 21 months ago by ▴ 10
0
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1
reply
864
views
Using DESeq2 only for normalization
DESeq2 Normalization
updated 21 months ago by ★ 4.6k • written 21 months ago by • 0
0
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1
reply
585
views
processing samples with significantly different counts
DESeq2 Normalization
updated 21 months ago by ★ 4.6k • written 21 months ago by • 0
0
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5
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1.7k
views
DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 21 months ago by ★ 4.6k • written 21 months ago by • 0
2
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3
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1.3k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 20 months ago by ★ 4.6k • written 21 months ago by ▴ 20
0
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1
reply
786
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 21 months ago by ★ 4.6k • written 21 months ago by • 0
50 results • Page 1 of 1
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Comment: Running multiple KNN queries in parallel by SamGG ▴ 360
Thank you for your detailed answer, I appreciate it and your work.
Answer: Running multiple KNN queries in parallel by Aaron Lun ★ 28k
That is correct - you can't pass the prebuilt objects to different processes. Maybe `MulticoreParam()` might work on POSIX systems but I'm …
Answer: RSubread output significantly different from bash Subread output by Gordon Smyth 52k
The difference (as ATpoint has correctly pointed out) is that Rsubread::featureCounts counts multi-mapping reads by default whereas the com…
Answer: Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square by Michael Love 43k
I would check the rank of your model matrix, and perhaps meet with a local statistician who can help you create an appropriate design matri…
Comment: sva: get a sv for RIN scores by gabriel.hoffman ▴ 170
Agreed. I'll add that with small sample size, a covariate can explain some fraction of expression variation even under the null.
Votes
Answer: Running multiple KNN queries in parallel
Answer: Running multiple KNN queries in parallel
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: How to annotate a limma Elist raw class object with an annotation file
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