Showing : normalization • reset
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Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization Lipidomics lipidr
5 weeks ago David R ▴ 90
3
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4
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640
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
6 weeks ago dseauer • 0
1
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2
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947
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
7 weeks ago Ai • 0
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0
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166
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Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
7 weeks ago kim • 0
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1
reply
377
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 8 weeks ago by ★ 4.6k • written 8 weeks ago by • 0
3
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4
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548
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
11 weeks ago Eva ▴ 10
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0
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183
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Background normalization of Diffbind dba.normalize
Normalization DiffBind
11 weeks ago Young Boqin • 0
1
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1
reply
263
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 3 months ago by ★ 4.6k • written 3 months ago by • 0
1
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5
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845
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 4 months ago by 52k • written 4 months ago by • 0
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2
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365
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 4 months ago by • 0
1
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3
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989
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
6 months ago Tanvi • 0
2
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2
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550
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Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 7 months ago by ▴ 10 • written 7 months ago by • 0
0
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2
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567
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
7 months ago sukeshinik5 ▴ 20
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1
reply
414
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 7 months ago by 43k • written 7 months ago by • 0
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1
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403
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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
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1.0k
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
8 months ago Henry ▴ 10
1
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6
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903
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 9 months ago by 43k • written 9 months ago by • 0
0
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2
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560
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
9 months ago Marianna ▴ 20
1
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4
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700
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EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
9 months ago samuel.channon • 0
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0
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409
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
10 months ago • updated 9 months ago Giovanni Calice ▴ 160
2
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1
reply
534
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 10 months ago by ★ 4.6k • written 10 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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704
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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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997
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 11 months ago by • 0
0
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1
reply
758
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 11 months ago by ★ 4.6k • written 11 months ago by • 0
2
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4
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1.5k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
11 months ago Sabiha ▴ 20
1
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1
reply
750
views
DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 11 months ago by 43k • written 12 months ago by • 0
2
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2
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2.1k
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
12 months ago • updated 11 months ago Linton • 0
0
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0
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506
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SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
13 months ago vasily.dobrovolsky • 0
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6
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1.6k
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
14 months ago erika.maldonado-rosado • 0
0
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0
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519
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
14 months ago Florian • 0
1
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11
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1.9k
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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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4.3k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 2.1 years ago by • 0
1
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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 18 months ago by 52k • written 18 months ago by • 0
0
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3
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873
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Normalization of different input materials
Normalization DESeq2
updated 18 months ago by ★ 4.6k • written 18 months ago by ▴ 10
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2
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1.2k
views
Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
19 months ago dwas • 0
5
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11
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5.2k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 19 months ago by ▴ 20
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3
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1.0k
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
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2
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1.3k
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
20 months ago Abdul ▴ 20
2
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2
replies
901
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
21 months ago Abdul ▴ 20
1
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2
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817
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 21 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
21 months ago Assa Yeroslaviz ★ 1.5k
1
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6
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2.4k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 16 months ago by 52k • written 4.3 years ago by ▴ 20
2
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3
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2.8k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 21 months ago by ★ 4.6k • written 21 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
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1
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886
views
Using DESeq2 only for normalization
DESeq2 Normalization
updated 21 months ago by ★ 4.6k • written 21 months ago by • 0
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1
reply
600
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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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1.8k
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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 21 months ago by ★ 4.6k • written 21 months ago by ▴ 20
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1
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804
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Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 22 months ago by ★ 4.6k • written 22 months ago by • 0
50 results • Page 1 of 1
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Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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