Showing : limma • reset
1
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 14 months ago by ▴ 40
0
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2
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851
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
14 months ago Tadeoye ▴ 20
0
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2
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1.1k
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 15 months ago by 53k • written 15 months ago by ▴ 10
2
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3
replies
2.0k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 15 months ago by 68k • written 15 months ago by ▴ 10
1
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2
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781
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contrast matrix design for a continuous variable
limma
15 months ago • updated 13 months ago dtzhu337 • 0
3
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3
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1.1k
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Crossover design with limma
limma crossover
updated 14 months ago by 53k • written 15 months ago by ▴ 30
0
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9
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2.0k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 15 months ago by 68k • written 15 months ago by • 0
6
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10
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3.9k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 14 months ago by ★ 5.0k • written 15 months ago by ▴ 10
1
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3
replies
882
views
Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 15 months ago by • 0
0
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2
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453
views
List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
15 months ago giulia.gentile ▴ 10
4
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2
replies
1.7k
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 15 months ago by 53k • written 15 months ago by ▴ 60
1
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2
replies
561
views
Limma Interaction Effect with Covariates
limma DMRcate
15 months ago kitzhu • 0
2
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3
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1.6k
views
[How to construct a model.matrix ]
limma modelmatrix
updated 15 months ago by 53k • written 15 months ago by • 0
3
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4
replies
1.3k
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
15 months ago dseauer • 0
1
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3
replies
1.1k
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
15 months ago abadgerw • 0
0
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5
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1.3k
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
15 months ago abadgerw • 0
1
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8
replies
3.0k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 16 months ago by • 0
1
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2
replies
1.5k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
16 months ago Ai • 0
3
votes
3
replies
1.8k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 16 months ago by • 0
4
votes
3
replies
1.3k
views
Analysis of 2*4 factorial design
limma
updated 16 months ago by 53k • written 16 months ago by • 0
2
votes
12
replies
3.0k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
16 months ago • updated 15 months ago john • 0
4
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6
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2.0k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 16 months ago by 53k • written 16 months ago by • 0
4
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6
replies
2.0k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
16 months ago altintas.ali • 0
2
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2
replies
1.3k
views
Automatically generate contrasts from a model matrix / formula
limma
updated 16 months ago by ★ 5.0k • written 16 months ago by ▴ 10
3
votes
3
replies
879
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
16 months ago Guido Hooiveld ★ 4.1k
0
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3
replies
844
views
Need help interpreting heatmaps from limma
limma
written 16 months ago by • 0
2
votes
1
reply
2.0k
views
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
limma
updated 16 months ago by 68k • written 16 months ago by ▴ 10
5
votes
4
replies
1.2k
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
1
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2
replies
1.0k
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 17 months ago by 43k • written 17 months ago by ▴ 10
0
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0
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548
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
17 months ago tim.meese • 0
0
votes
2
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931
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 17 months ago by 53k • written 17 months ago by • 0
0
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2
replies
770
views
Question on performing ANOVA-like analysis using limma
limma
updated 17 months ago by 53k • written 17 months ago by • 0
17
votes
9
replies
8.6k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 17 months ago by 68k • written 9.8 years ago by ▴ 10
2
votes
1
reply
957
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 17 months ago by 68k • written 17 months ago by ▴ 20
0
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1
reply
2.7k
views
Unable to install/use limma
limma Bioconductor
updated 18 months ago by 68k • written 18 months ago by • 0
3
votes
3
replies
1.1k
views
voom does not seem to properly correct for library size
limma
updated 18 months ago by 53k • written 18 months ago by ★ 5.0k
1
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5
replies
1.9k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 18 months ago by 53k • written 18 months ago by • 0
0
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3
replies
1.1k
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 18 months ago by 53k • written 18 months ago by • 0
4
votes
6
replies
1.7k
views
using limma trend workflow in CAMERA
CAMERA limma
updated 25 days ago by 53k • written 18 months ago by • 0
3
votes
3
replies
1.1k
views
One-sided tests with CAMERA-PR
CAMERA limma
updated 18 months ago by 53k • written 18 months ago by ▴ 10
1
vote
6
replies
1.5k
views
limma and Syntactically Invalid Factor Values
limma
updated 19 months ago by 53k • written 19 months ago by ★ 1.6k
1
vote
1
reply
1.2k
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
19 months ago Bioinformagician • 0
5
votes
3
replies
1.2k
views
Limma comparing gene expression between base line and one treatment
limma
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
1
reply
1.3k
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
2
votes
5
replies
1.3k
views
Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by • 0
4
votes
14
replies
2.8k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign limma pairedsamples
updated 19 months ago by 53k • written 19 months ago by • 0
3
votes
4
replies
1.4k
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma dreamlet
20 months ago jcollier • 0
4
votes
4
replies
1.9k
views
Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma adjustment voom removeBatchEffect covariates
20 months ago sukeshinik5 ▴ 20
0
votes
1
reply
633
views
Deseq2 design matrix
DESeq2 Designmatrix limma
updated 20 months ago by 68k • written 20 months ago by • 0
4
votes
4
replies
1.3k
views
Warning message when running limma with covariates
limma
20 months ago • updated 14 months ago Chris ▴ 20
4,232 results • Page 2 of 85
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Answer: Unable to find ENTREZ IDs by James W. MacDonald 68k
Those are the 'symbols', and are a concatenation of LOC and the NCBI Gene ID (what used to be called an Entrez Gene ID). As an example:http…
Answer: Inconsistencies between accessor functions for TxDb databases with selected seql by a2a2hd42aa • 0
Technical inconsistencies in database accessors can disrupt your workflow, but finding a reliable source to download online mobile games sh…
Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Votes
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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