Showing : Normalization • reset
0
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gene detection across experiments
DESeq2 Normalization
9 weeks ago Mara • 0
0
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3
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1.5k
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RNA-seq: TPM batch effect correction
rnaseqDTU Normalization
updated 9 weeks ago by 68k • written 9 weeks ago by • 0
0
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5
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685
views
WGCNA
WGCNA Normalization RNASeq
written 6 months ago by • 0
0
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2
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453
views
Meffil: error in functional normalization function (Error in rg.to.mu(rg, probes))
methylationArrayAnalysis Normalization Epigenetics MethylationArrayData
6 months ago a.alkema • 0
6
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5
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953
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 7 months ago by 68k • written 8 months ago by • 0
0
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0
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298
views
Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization Lipidomics lipidr
9 months ago David R ▴ 90
3
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4
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1.1k
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
9 months ago dseauer • 0
1
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2
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1.3k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
10 months ago Ai • 0
0
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0
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502
views
Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
10 months ago kim • 0
0
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1
reply
831
views
Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 10 months ago by ★ 4.9k • written 10 months ago by • 0
3
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4
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1.1k
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
10 months ago Eva ▴ 10
0
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0
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509
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Background normalization of Diffbind dba.normalize
Normalization DiffBind
10 months ago Young Boqin • 0
1
vote
1
reply
501
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 11 months ago by ★ 4.9k • written 11 months ago by • 0
1
vote
5
replies
1.3k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 12 months ago by 52k • written 12 months ago by • 0
0
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2
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597
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 12 months ago by • 0
1
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3
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1.8k
views
Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
14 months ago Tanvi • 0
2
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2
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792
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 15 months ago by ▴ 10 • written 15 months ago by • 0
0
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2
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894
views
Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
15 months ago sukeshinik5 ▴ 20
0
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1
reply
677
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 15 months ago by 43k • written 15 months ago by • 0
0
votes
1
reply
657
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 16 months ago by ★ 4.9k • written 16 months ago by • 0
2
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2
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1.6k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
16 months ago Henry ▴ 10
1
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6
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1.5k
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 17 months ago by 43k • written 17 months ago by • 0
0
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2
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842
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
17 months ago Marianna ▴ 20
1
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4
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1.0k
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
17 months ago samuel.channon • 0
0
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0
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564
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
18 months ago • updated 17 months ago Giovanni Calice ▴ 160
2
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1
reply
719
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 18 months ago by ★ 4.9k • written 18 months ago by • 0
2
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2
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1.6k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
19 months ago jackafiore • 0
2
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3
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982
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 19 months ago by 68k • written 19 months ago by • 0
1
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3
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1.2k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 19 months ago by • 0
0
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1
reply
1.1k
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 19 months ago by ★ 4.9k • written 19 months ago by • 0
2
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4
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2.0k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
19 months ago Sabiha ▴ 20
1
vote
1
reply
972
views
DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 20 months ago by 43k • written 20 months ago by • 0
2
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2
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3.5k
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
20 months ago Linton • 0
0
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0
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731
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
21 months ago vasily.dobrovolsky • 0
0
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6
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2.2k
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
22 months ago erika.maldonado-rosado • 0
0
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0
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674
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
22 months ago Florian • 0
1
vote
11
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2.8k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
1
vote
4
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5.7k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 2.8 years ago by • 0
1
vote
5
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1.9k
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 2.2 years ago by 52k • written 2.2 years ago by • 0
0
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3
replies
1.1k
views
Normalization of different input materials
Normalization DESeq2
updated 2.2 years ago by ★ 4.9k • written 2.2 years ago by ▴ 10
0
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2
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1.4k
views
Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
2.3 years ago dwas • 0
5
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11
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7.2k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 2.3 years ago by ▴ 20
0
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3
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1.2k
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 2.3 years ago by 68k • written 2.3 years ago by • 0
1
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2
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1.6k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
2.4 years ago Abdul ▴ 20
2
votes
2
replies
1.1k
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
2.4 years ago Abdul ▴ 20
1
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2
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961
views
RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 2.4 years ago by • 0
0
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2
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1.5k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.4 years ago Assa Yeroslaviz ★ 1.5k
1
vote
6
replies
2.9k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 2.1 years ago by 52k • written 5.0 years ago by ▴ 20
2
votes
3
replies
3.5k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 2.4 years ago by ★ 4.9k • written 2.4 years ago by ▴ 10
2
votes
1
reply
1.9k
views
deseq2 RLE normalization
RLE normalization deseq2
updated 2.5 years ago by ★ 4.9k • written 2.5 years ago by ▴ 10
1,761 results • Page 1 of 36
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Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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