Showing : Limma • reset
0
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11
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2.3k
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limma::contrast.fit() potential bugs when weights from voom() included
bugs limma
3.2 years ago Zhenyu • 0
2
votes
3
replies
1.2k
views
limma::goana - "Invalid value for odds"
limma
updated 3.2 years ago by 53k • written 3.2 years ago by ▴ 30
0
votes
0
replies
879
views
Finding DEGs between two different datasets using limma
Proteomics limma proteomi
3.2 years ago mfaleevs • 0
5
votes
6
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2.5k
views
Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
0
votes
0
replies
799
views
Tuning the MetaVolcanoR plots
limma MetaVolcanoR
3.2 years ago JAcky • 0
1
vote
10
replies
3.9k
views
multiple voom runs with duplicateCorrelation and negative values in limma
limma voom
3.2 years ago Hilary ▴ 40
0
votes
3
replies
1.5k
views
Design and contrast matrices for analyzing the effect of two factors of interest on protein expression, controlling for factors and covariates not of…
limma Proteomics ProteomicsWorkflow
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
2
votes
2
replies
1.1k
views
paired samples, comparing expression given a continuous variable
limma
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
1
vote
1
reply
879
views
ordinal treatment group design / contrast matrix
limma
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
0
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1
reply
1.4k
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
1
vote
1
reply
922
views
IS DGE possible with normalized microarray expression data and Limma ?
limma MicroarrayData
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
2
votes
2
replies
2.0k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
3.3 years ago Yang Shi ▴ 10
2
votes
4
replies
2.1k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 3.3 years ago by 53k • written 3.3 years ago by ▴ 10
5
votes
6
replies
2.7k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
3.3 years ago Yang Shi ▴ 10
2
votes
4
replies
2.7k
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
3.3 years ago Yang Shi ▴ 10
0
votes
0
replies
946
views
MetaVolcanoR usage
limma MetaVolcanoR EnhancedVolcano
3.3 years ago JAcky • 0
3
votes
4
replies
1.5k
views
Can I use limma::avereps to remove dupicated genes before conduct DEG based on RSEM Expected_count data?
limma RNASeq Expected_count DESeq2
3.3 years ago Yang Shi ▴ 10
1
vote
1
reply
1.0k
views
Weight Array Quality before of after applying variance filtering?
limma arrays genefilter
updated 3.3 years ago by 68k • written 3.3 years ago by ▴ 40
2
votes
6
replies
2.0k
views
Limma beta coefficient confidence intervals
limma limmaGUI beta
3.4 years ago fluentin44 • 0
0
votes
1
reply
1.2k
views
Compare different cell lines with tissues using limma
limma MicroarrayData Microarray Agilent
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
3
votes
9
replies
2.9k
views
Help with limma contrast, difference of a difference?
limma
3.4 years ago Ahdee ▴ 60
0
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8
replies
2.2k
views
Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
3.4 years ago YC • 0
0
votes
3
replies
3.1k
views
Problem in kegga() and others getting data from KEGG after switch from http to https
limma KEGGREST EGSEA
updated 3.4 years ago by 4.2k • written 3.4 years ago by ★ 2.0k
0
votes
2
replies
949
views
Get confused about the mean log-intensity (Amean)
limma
3.4 years ago OE • 0
2
votes
9
replies
4.0k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
3.4 years ago Peipei • 0
1
vote
8
replies
2.3k
views
edgeR design matrix with multiple cell types and combination treatments
DifferentialExpression celltype treatment edgeR limma
3.4 years ago giBio • 0
0
votes
2
replies
1.5k
views
How do I remove the outlier probes highlighted in the plotSA function of limma
limma
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
1
vote
2
replies
1.3k
views
Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
3.4 years ago Mikołaj Mierzejewski • 0
1
vote
2
replies
1.8k
views
Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
3.4 years ago Mikołaj Mierzejewski • 0
2
votes
1
reply
2.1k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma BatchEffect
updated 3.4 years ago by 53k • written 3.4 years ago by ▴ 70
6
votes
2
replies
3.2k
views
Pseudo-bulk Limma Approaches
limma
updated 3.4 years ago by 53k • written 3.5 years ago by ▴ 370
9
votes
3
replies
9.6k
views
Limma vs deseq2 results
limma RNASeq R
3.5 years ago • updated 3.4 years ago k___ ▴ 30
2
votes
2
replies
1.4k
views
Help with constructing design matrix for edgeR/limma
limma design.matrix model.matrix edgeR
3.5 years ago • updated 3.4 years ago adrianna_07 • 0
1
vote
4
replies
1.5k
views
How to figure out the FC value from Limma
limma DEGseq DifferentialExpression
updated 3.5 years ago by ★ 4.0k • written 3.5 years ago by • 0
1
vote
1
reply
1.4k
views
Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma lmfit R DifferentialExpression
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
3
votes
3
replies
2.4k
views
Question on RNA-Seq single sample data analysis in EdgeR
R edgeR limma RNASeq Normalization
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 10
0
votes
6
replies
2.0k
views
regression analysis for epic array methylation data using limma
limma Epigenetics STATISTICS R
3.5 years ago Jitendra ▴ 10
0
votes
2
replies
1.6k
views
Using limma to read Illumina HT-12 v4 data
limma
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
4
votes
6
replies
2.3k
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2 Transcriptomics Visualization R limma
3.5 years ago mohammedtoufiq91 ▴ 10
3
votes
4
replies
2.7k
views
Quantile Normalization after rma or not?
limma Microarray oligo
3.5 years ago Yang Shi ▴ 10
2
votes
2
replies
2.6k
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 10
1
vote
2
replies
1.5k
views
toptable sort .by set
limma rnaseqGene
3.5 years ago snowmattin • 0
1
vote
5
replies
3.1k
views
Unsuccessful DE analysis using limma - voom
limma
3.5 years ago JAcky • 0
2
votes
1
reply
1.6k
views
Extremely low P-values when using Limma on high sample size proteomics data
limma Proteomics
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
2
votes
1
reply
1.1k
views
Limma model orientation
limma methylation MethylationArray
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
2
votes
4
replies
1.8k
views
Overfitting in limma
limma Regression overfitting
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 30
0
votes
0
replies
785
views
diffcyt - topTable function returns one total significance estimate instead of one per comparison
limma diffcyt edgeR
3.5 years ago stefanos.bamopoulos • 0
2
votes
4
replies
5.1k
views
Limma: How to deal with multiple batch effects and what is going on under the hood
limma voom
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 20
0
votes
3
replies
1.0k
views
Limma time course with several conditions
limma
3.5 years ago rina ▴ 30
0
votes
7
replies
1.9k
views
Which Limma guide is recommended ?
limma R DifferentialExpression
3.6 years ago • updated 3.5 years ago JAcky • 0
4,225 results • Page 7 of 85
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Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated by RalphSavage99 • 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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