Showing : voom • reset
0
votes
1
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164
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Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 8 weeks ago by 47k • written 8 weeks ago by • 0
3
votes
4
replies
373
views
Processing data with voom "expression values" and "weights"
limma voom
updated 4 months ago by 47k • written 4 months ago by • 0
0
votes
1
reply
206
views
Alternatives to Voom in experiments without replicate
limma edgeR Voom
updated 5 months ago by 47k • written 5 months ago by • 0
0
votes
3
replies
416
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
1
reply
236
views
Voom variance values: Some minor confusion about which variance is fed to lowess when using a design matrix of covariates
voom
updated 6 months ago by 47k • written 6 months ago by • 0
1
vote
10
replies
858
views
multiple voom runs with duplicateCorrelation and negative values in limma
limma voom
9 months ago Hilary ▴ 30
2
votes
2
replies
507
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
10 months ago Yang Shi ▴ 10
2
votes
4
replies
719
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 10 months ago by 47k • written 10 months ago by ▴ 10
5
votes
6
replies
768
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
10 months ago Yang Shi ▴ 10
2
votes
4
replies
525
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
10 months ago Yang Shi ▴ 10
2
votes
9
replies
1.2k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
11 months ago Peipei • 0
2
votes
2
replies
649
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 12 months ago by 47k • written 12 months ago by ▴ 10
2
votes
4
replies
1.3k
views
Limma: How to deal with multiple batch effects and what is going on under the hood
limma voom
updated 13 months ago by 47k • written 13 months ago by ▴ 20
0
votes
3
replies
759
views
limma voom contrasts
contrasts limma voom
updated 15 months ago by 47k • written 15 months ago by ▴ 90
0
votes
3
replies
630
views
Need help with a contrast design for limma with a missing group?
limma VOOM
updated 15 months ago by 47k • written 15 months ago by ▴ 50
3
votes
5
replies
1.5k
views
limma-trend and voom results do not agree
limma limma-trend voom RNASeq
18 months ago Tyler Sagendorf ▴ 10
3
votes
2
replies
786
views
Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
18 months ago altintas.ali • 0
0
votes
2
replies
1.1k
views
Mean-variance trend and identifying significant DE with large amount of biological change in expression in time-series data
voom
19 months ago • updated 17 months ago hmviit • 0
0
votes
2
replies
803
views
voom flips the sign relative to log(cpm)
limma limma-voom rnaseq voom
updated 20 months ago by 47k • written 20 months ago by • 0
0
votes
1
reply
954
views
limma/voom for protein intensity data
limma proteomics voom
updated 21 months ago by ★ 2.9k • written 21 months ago by ▴ 60
0
votes
2
replies
642
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
21 months ago James • 0
0
votes
2
replies
590
views
voom-limma workflow for RNAseq samples with very different numbers of counts
voom limma RNASeq
2.2 years ago annadv • 0
0
votes
2
replies
3.2k
views
TPM data in limma/voom
voom limma DifferentialExpression edgeR
2.3 years ago RJM • 0
1
vote
1
reply
1.0k
views
Limma-Voom - Time series experiment with one group (duplicateCorrelation() function)
voom duplicateCorrelation() timeseries limma
updated 2.4 years ago by 47k • written 2.4 years ago by ▴ 10
6
votes
13
replies
3.4k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 10 months ago by 47k • written 2.8 years ago by ▴ 60
0
votes
5
replies
784
views
isoform data, deep sequencing and voom
isoform deep sequencing voom
updated 2.8 years ago by 47k • written 2.8 years ago by ▴ 620
0
votes
4
replies
654
views
mean-variance trend plots with isoform and gene-level data from tximport
tximport isoform voom
updated 2.9 years ago by 47k • written 2.9 years ago by ▴ 620
1
vote
4
replies
600
views
How to compare a single RNA-Seq sample with microarray samples?
voom rna-seq microarray
updated 3.0 years ago by 63k • written 3.0 years ago by ▴ 10
0
votes
1
reply
487
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 3.0 years ago by 47k • written 3.0 years ago by • 0
2
votes
6
replies
1.4k
views
linear mixed models using edgeR+limma
linear mixed model edger limma voom RNA-seq
updated 3.0 years ago by 47k • written 3.0 years ago by • 0
1
vote
5
replies
876
views
Limma for proteomic data! Please Help!
limma voom lmfit ebayesfit
updated 3.1 years ago by 47k • written 3.1 years ago by • 0
0
votes
2
replies
379
views
estimating variability in absence of replicates for edgeR
edgeR RNAseq voom variability estimator
updated 3.2 years ago by 47k • written 3.2 years ago by • 0
3
votes
6
replies
1.0k
views
paired and unpaired test at the same time with voom limma
limma voom rna-seq paired test unpaired test
updated 3.2 years ago by 47k • written 3.2 years ago by • 0
6
votes
5
replies
1.4k
views
How to know if I should use voomWithQualityWeights() or not?
limma RNA-Seq voom voomWithQualityWeights edgeR
updated 3.2 years ago by 47k • written 3.2 years ago by • 0
0
votes
0
replies
478
views
RNAseq/miRNAseq normalization for calculating gene correlations, survival analysis, and exploratory graphing
limma edger voom rnaseq mirnaseq
3.3 years ago atakanekiz ▴ 30
4
votes
7
replies
1.1k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 3.5 years ago by 47k • written 3.5 years ago by ▴ 50
3
votes
6
replies
2.1k
views
Understanding voom behavior when model matrix is used with/without intercept for a continuous variable
limma voom rnaseq model.matrix intercept
updated 3.5 years ago by 47k • written 3.5 years ago by ▴ 30
0
votes
0
replies
565
views
limma-voom group design and its effect on sva
limma voom group-design sva
3.5 years ago kentfung ▴ 10
2
votes
4
replies
844
views
Limma gives big p-values for large LFC
limma voom
updated 3.6 years ago by 47k • written 3.6 years ago by • 0
4
votes
5
replies
671
views
Defining the design for a complicated multi-level experiment in Limma
limma RNASeq R voom
updated 3.6 years ago by 63k • written 3.6 years ago by ▴ 50
0
votes
1
reply
942
views
Variance unstable after fitting to linear model with limma-voom pipeline
limma voom
3.7 years ago kentfung ▴ 10
4
votes
3
replies
1.2k
views
Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancePartition dream
updated 3.7 years ago by ▴ 90 • written 3.9 years ago by ▴ 50
0
votes
3
replies
578
views
Design matrix for cohort with samples outside "block"
limma voom sva
3.8 years ago kentfung ▴ 10
0
votes
3
replies
624
views
How to apply a linear mixed model onto an RNA-Seq data?
limma linear mixed model voom rna-seq
3.8 years ago Assa Yeroslaviz ★ 1.5k
4
votes
4
replies
670
views
normalization of RNA-seq data after over-expressing the transcription factors
limma deseq2 voom edgeR
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ▴ 660
3
votes
4
replies
1.5k
views
MDS plotting within the limma/voom workflow
limma voom deseq2
updated 3.9 years ago by 47k • written 4.0 years ago by ▴ 50
1
vote
5
replies
819
views
Time course experiment using limma with voom
limma voom RNA Seq Time-course experiments
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
2
votes
2
replies
698
views
voomWithQualityWeights together with covariate in design matrix
limma voom RNA-seq voomWithQualityWeights
updated 4.0 years ago by ▴ 1000 • written 4.0 years ago by ▴ 90
1
vote
2
replies
758
views
Why does limma voom E value give different result than the voom object
limma voom rna-seq
updated 4.1 years ago by ▴ 160 • written 4.1 years ago by ▴ 50
5
votes
7
replies
1.6k
views
limma - blocking or regressing out nuisance variable
limma voom RNA-seq
updated 4.1 years ago by 63k • written 4.1 years ago by ▴ 20
50 results • Page 1 of 1
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Answer: Ensembl plants at annotationHub? by Bruno • 0
Hi Johannes, First, thank you so much for providing these annotations for the community. We feel often a bit left off in the plant commu…
Comment: DESeq2 on multilevel design variable by swbarnes2 ★ 1.2k
Did you relevel before or after calling DESeq?
Comment: SummarizedExperiment is now warning on attach about `read_block` namespace confl by Hervé Pagès 16k
Available since last Friday. See https://bioconductor.org/packages/3.17/DelayedArray
Comment: Diffbind "No genome detected" by James W. MacDonald 63k
The error you see comes from an internal function called `pv.genome` that inspects the header of your BAM file and tries to infer the genom…
Comment: Diffbind "No genome detected" by kyliecode • 0
Hi James, Thanks for your reply! For the blacklist, I just used the one provided by DiffBind, which is "DBA_BLACKLIST_MM10". For the grey…
Votes
Answer: DESeq2 on multilevel design variable
Comment: Sudden error with KEGG analysis using gometh
Comment: Sudden error with KEGG analysis using gometh
Answer: Although I successfully installed the package "simpleaffy'' , I cannot library i
Answer: Annotation with org.Hs.eg.db Genome Build 38
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