Showing : LIMMA • reset
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bigwig to counts
DESeq2 edgeR bigwig limma
3.3 years ago • updated 3.0 years ago Bogdan ▴ 670
1
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1
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1.4k
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Weird distribution of p-values, with no significant adjusted p-values?
fdr limmaGUI p-values limma
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
0
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7
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2.2k
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Help with differential gene expression using Agilent Microarray data (from GEO database)
limma Paireddata DifferentialExpression
updated 3.2 years ago by 68k • written 3.3 years ago by • 0
1
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2
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1.8k
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Limma adj.p.value the same for many different p.values
limmaGUI limma adj.p.value StatisticalMethod
3.3 years ago walkerrh95 • 0
3
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7
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3.1k
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Different results between Limma and DESEQ2 for Differential Expression Analysis
DESeq2 limma
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by ▴ 50
5
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8
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3.1k
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Question on performing filtering by gene expression on a normalized matrix in limma?
expression R filtering limma
3.3 years ago • updated 3.1 years ago mohammedtoufiq91 ▴ 10
0
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11
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2.4k
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limma::contrast.fit() potential bugs when weights from voom() included
bugs limma
3.4 years ago Zhenyu • 0
2
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3
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1.3k
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limma::goana - "Invalid value for odds"
limma
updated 3.4 years ago by 53k • written 3.4 years ago by ▴ 30
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0
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959
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Finding DEGs between two different datasets using limma
Proteomics limma proteomi
3.4 years ago mfaleevs • 0
5
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6
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2.7k
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Selecting individual samples from tximport and DGE matrix design with missing biological replicate
DESeq2 limma tximport
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
0
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0
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835
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Tuning the MetaVolcanoR plots
limma MetaVolcanoR
3.4 years ago JAcky • 0
1
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10
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4.3k
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multiple voom runs with duplicateCorrelation and negative values in limma
limma voom
3.4 years ago Hilary ▴ 40
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3
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1.6k
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 3.4 years ago by 53k • written 3.4 years ago by • 0
2
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2
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1.2k
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paired samples, comparing expression given a continuous variable
limma
updated 3.4 years ago by 53k • written 3.5 years ago by • 0
1
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1
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934
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ordinal treatment group design / contrast matrix
limma
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
0
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1
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1.5k
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Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData BatchEffect r limma
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
1
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1
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964
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IS DGE possible with normalized microarray expression data and Limma ?
limma MicroarrayData
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
2
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2
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2.1k
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How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
3.5 years ago Yang Shi ▴ 10
2
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4
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2.2k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 10
5
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6
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2.8k
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Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
3.5 years ago Yang Shi ▴ 10
2
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4
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2.8k
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
3.5 years ago Yang Shi ▴ 10
0
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0
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1000
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MetaVolcanoR usage
limma MetaVolcanoR EnhancedVolcano
3.5 years ago JAcky • 0
3
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4
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1.6k
views
Can I use limma::avereps to remove dupicated genes before conduct DEG based on RSEM Expected_count data?
limma RNASeq Expected_count DESeq2
3.5 years ago Yang Shi ▴ 10
1
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1
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1.1k
views
Weight Array Quality before of after applying variance filtering?
limma arrays genefilter
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 40
2
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6
replies
2.1k
views
Limma beta coefficient confidence intervals
limma limmaGUI beta
3.6 years ago fluentin44 • 0
0
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1
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1.3k
views
Compare different cell lines with tissues using limma
limma MicroarrayData Microarray Agilent
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
3
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9
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3.1k
views
Help with limma contrast, difference of a difference?
limma
3.6 years ago Ahdee ▴ 60
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8
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2.3k
views
Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
3.6 years ago YC • 0
0
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3
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3.3k
views
Problem in kegga() and others getting data from KEGG after switch from http to https
limma KEGGREST EGSEA
updated 3.6 years ago by 4.3k • written 3.6 years ago by ★ 2.0k
0
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2
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1.1k
views
Get confused about the mean log-intensity (Amean)
limma
3.6 years ago OE • 0
2
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9
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4.3k
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Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
3.6 years ago Peipei • 0
1
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8
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2.4k
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edgeR design matrix with multiple cell types and combination treatments
DifferentialExpression celltype treatment edgeR limma
3.6 years ago giBio • 0
0
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2
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1.6k
views
How do I remove the outlier probes highlighted in the plotSA function of limma
limma
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
1
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2
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1.4k
views
Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
3.6 years ago Mikołaj Mierzejewski • 0
1
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2
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2.0k
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Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
3.6 years ago Mikołaj Mierzejewski • 0
2
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1
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2.2k
views
removeBatchEffect: Coefficients not estimable when using "batch matrix" for `covariates` argument.
limma BatchEffect
updated 3.6 years ago by 53k • written 3.6 years ago by ▴ 70
6
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2
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3.6k
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Pseudo-bulk Limma Approaches
limma
updated 3.6 years ago by 53k • written 3.6 years ago by ▴ 370
9
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3
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10k
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Limma vs deseq2 results
limma RNASeq R
3.7 years ago • updated 3.6 years ago k___ ▴ 30
2
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2
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1.4k
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Help with constructing design matrix for edgeR/limma
limma design.matrix model.matrix edgeR
3.7 years ago • updated 3.6 years ago adrianna_07 • 0
1
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4
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1.6k
views
How to figure out the FC value from Limma
limma DEGseq DifferentialExpression
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
1
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1
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1.4k
views
Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma lmfit R DifferentialExpression
updated 3.7 years ago by ★ 5.0k • written 3.7 years ago by • 0
3
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3
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2.5k
views
Question on RNA-Seq single sample data analysis in EdgeR
R edgeR limma RNASeq Normalization
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 10
0
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6
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2.1k
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regression analysis for epic array methylation data using limma
limma Epigenetics STATISTICS R
3.7 years ago Jitendra ▴ 10
0
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2
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1.8k
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Using limma to read Illumina HT-12 v4 data
limma
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
4
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6
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2.5k
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How to best visualize multi-level transcriptomics experiment data?
ggplot2 Transcriptomics Visualization R limma
3.7 years ago mohammedtoufiq91 ▴ 10
3
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4
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2.9k
views
Quantile Normalization after rma or not?
limma Microarray oligo
3.7 years ago Yang Shi ▴ 10
2
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2
replies
2.8k
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 10
1
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2
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1.5k
views
toptable sort .by set
limma rnaseqGene
3.7 years ago snowmattin • 0
1
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5
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3.3k
views
Unsuccessful DE analysis using limma - voom
limma
3.7 years ago JAcky • 0
2
votes
1
reply
1.7k
views
Extremely low P-values when using Limma on high sample size proteomics data
limma Proteomics
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
4,230 results • Page 7 of 85
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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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