Showing : normalization • reset
0
votes
1
reply
81
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 3 days ago by 42k • written 4 days ago by • 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 7 days ago by • 0 • written 16 months ago by ▴ 10
0
votes
1
reply
97
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 8 days ago by ★ 4.1k • written 8 days ago by • 0
2
votes
2
replies
416
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
5 weeks ago Henry ▴ 10
1
vote
6
replies
457
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
0
votes
2
replies
195
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 weeks ago Marianna ▴ 20
1
vote
4
replies
312
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
8 weeks ago samuel.channon • 0
0
votes
0
replies
168
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
10 weeks ago • updated 8 weeks ago Giovanni Calice ▴ 160
6
votes
11
replies
4.0k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 9 weeks ago by • 0 • written 3.2 years ago by ▴ 40
2
votes
1
reply
320
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
2
votes
2
replies
437
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
2
votes
3
replies
386
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
1
vote
3
replies
620
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 3 months ago by • 0
0
votes
1
reply
331
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
2
votes
4
replies
645
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
1
vote
1
reply
449
views
DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 4 months ago by 42k • written 4 months ago by • 0
2
votes
2
replies
710
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
4 months ago Linton • 0
0
votes
1
reply
1.5k
views
EdgeR norm.factor input
Normalization edgeR Normalization edgeR
updated 5 months ago by 50k • written 10.3 years ago by ★ 13k
4
votes
4
replies
2.1k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 5 months ago by 50k • written 2.4 years ago by ▴ 10
0
votes
0
replies
266
views
SomaticSignatures normalization for trinucleotide motifs in reference genome
Normalization SomaticSignatures
6 months ago vasily.dobrovolsky • 0
0
votes
3
replies
2.5k
views
Background correction with neqc
Normalization Cancer Normalization Cancer
updated 6 months ago by 50k • written 12.4 years ago by ★ 13k
0
votes
6
replies
919
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
2
votes
5
replies
11k
views
Conversion from counts to FPKM
counts fpkm fpkm() normalization deseq2
updated 7 months ago by • 0 • written 5.4 years ago by • 0
0
votes
0
replies
298
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
7 months ago Florian • 0
1
vote
11
replies
1.1k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 7 months ago by 42k • written 7 months ago by • 0
1
vote
4
replies
2.7k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 18 months ago by • 0
0
votes
2
replies
2.3k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 8 months ago by • 0 • written 2.1 years ago by • 0
1
vote
6
replies
1.8k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 9 months ago by 50k • written 3.7 years ago by ▴ 20
1
vote
5
replies
1.1k
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 10 months ago by 50k • written 10 months ago by • 0
0
votes
3
replies
620
views
Normalization of different input materials
Normalization DESeq2
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 10
0
votes
2
replies
778
views
Can VST-transformed community composition data be expressed as relative abundance?
vst relativeabundance Normalization DESeq2
11 months ago dwas • 0
5
votes
11
replies
3.2k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 11 months ago by ▴ 20
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 11 months ago by 50k • written 17 months ago by ▴ 20
0
votes
3
replies
730
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 12 months ago by 65k • written 12 months ago by • 0
1
vote
2
replies
914
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
13 months ago Abdul ▴ 20
2
votes
2
replies
679
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
13 months ago Abdul ▴ 20
2
votes
6
replies
2.5k
views
RNA-seq analysis across different experiments
limma deseq2 normalization degenes design and contrast matrix
written 6.8 years ago by ▴ 10
1
vote
2
replies
625
views
RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 13 months ago by • 0
0
votes
2
replies
749
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
13 months ago Assa Yeroslaviz ★ 1.5k
2
votes
3
replies
1.9k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 13 months ago by ★ 4.1k • written 14 months ago by • 0
2
votes
3
replies
930
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 14 months ago by ★ 4.1k • written 14 months ago by ▴ 20
9
votes
10
replies
6.9k
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 14 months ago by ▴ 10 • written 3.6 years ago by ▴ 10
0
votes
5
replies
1.2k
views
DESeq Normalization and miRNAs Filtering
DESeq2 Normalization
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
1
vote
1
reply
1.0k
views
deseq2 RLE normalization
RLE normalization deseq2
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
votes
1
reply
561
views
Using DESeq2 only for normalization
DESeq2 Normalization
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
votes
1
reply
418
views
processing samples with significantly different counts
DESeq2 Normalization
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
votes
2
replies
1.0k
views
best way to normalize for differences in sample read depth: normalize genome vs cn.MOPs
cn.mops normalization
updated 14 months ago by • 0 • written 6.2 years ago by • 0
0
votes
1
reply
556
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
votes
2
replies
753
views
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
15 months ago rcreswell01 • 0
3
votes
3
replies
813
views
What is cpmByGroup used for?
edgeR Normalization
updated 15 months ago by 65k • written 15 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Awards • All
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Popular Question to shepherl 3.9k
Popular Question to Ken C • 0
Popular Question to Johannes Rainer ★ 2.0k
Locations • All
WEHI, Melbourne, Australia, 23 minutes ago
United States, 43 minutes ago
United States, 47 minutes ago
San Diego, 56 minutes ago
Sweden, 1 hour ago
Traffic: 722 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6