Showing : Limma • reset
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limma and Syntactically Invalid Factor Values
limma
updated 2 days ago by 51k • written 5 days ago by ★ 1.5k
1
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1
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188
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DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
6 days ago • updated 3 days ago Bioinformagician • 0
3
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3
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193
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Limma comparing gene expression between base line and one treatment
limma
updated 7 days ago by 66k • written 8 days ago by • 0
0
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1
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117
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How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 8 days ago by ★ 4.2k • written 8 days ago by • 0
2
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5
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263
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 3 days ago by 66k • written 9 days ago by • 0
3
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8
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629
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LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign limma pairedsamples
updated 2 days ago by 66k • written 11 days ago by • 0
3
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4
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526
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Differences in Limma and Dreamlet random effects from confounded dataset
limma dreamlet
18 days ago • updated 17 days ago jcollier • 0
4
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4
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813
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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
4 weeks ago sukeshinik5 • 0
0
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1
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172
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Deseq2 design matrix
DESeq2 Designmatrix limma
updated 4 weeks ago by 66k • written 4 weeks ago by • 0
3
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3
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255
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Warning message when running limma with covariates
limma
updated 4 weeks ago by 51k • written 4 weeks ago by ▴ 20
0
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8
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1.2k
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limma comparison for small sample size and how to get covariance matrix
covariancematrix limma
5 weeks ago • updated 14 days ago jiachengd • 0
5
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4
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333
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Limma with covariates
limma
5 weeks ago Chris ▴ 20
3
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13
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904
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Limma model.matrix design with batch effect and different life stages proportion estimates
DeconRNASeq limma
updated 6 weeks ago by • 0 • written 6 weeks ago by • 0
2
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2
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290
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
9 weeks ago mohammedtoufiq91 ▴ 10
1
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2
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251
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Subsetting RNAseq data | voomaByGroup()
limma
9 weeks ago Anna • 0
1
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2
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402
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
11 weeks ago Dylan.Sheerin • 0
2
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2
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410
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error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
11 weeks ago • updated 10 weeks ago user_bioinfo • 0
3
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10
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735
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Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 11 weeks ago by 66k • written 11 weeks ago by • 0
3
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2
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581
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 8 weeks ago by 51k • written 12 weeks ago by • 0
0
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1
reply
241
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Gene-by-sample covariates in limma
Metabolomics limma
updated 12 weeks ago by 51k • written 12 weeks ago by • 0
3
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4
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379
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Help with error using camera() in limma
CAMERA limma
12 weeks ago Chris ▴ 20
0
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3
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371
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 12 weeks ago by 66k • written 12 weeks ago by • 0
0
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2
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291
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 3 months ago by • 0
0
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2
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367
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
3 months ago catv • 0
15
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17
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1.6k
views
Why p value inconsistent when using different number of pathway score?
limma
3 months ago • updated 12 weeks ago Chris ▴ 20
5
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3
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493
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Log-cpm values from limma
limma edgeR RNASeq
updated 11 weeks ago by 51k • written 3 months ago by • 0
0
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7
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629
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
3 months ago hortense96 • 0
1
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3
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472
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 3 months ago by 51k • written 3 months ago by • 0
5
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9
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1.2k
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Light difference when using coef vs omit a group when compare 3 groups.
limma
3 months ago Chris ▴ 20
2
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6
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863
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
3 months ago Chris ▴ 20
0
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1
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250
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Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 3 months ago by 51k • written 3 months ago by • 0
0
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4
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435
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Help with design.matrix
limma
3 months ago andrea.rodriguez-martinez13 • 0
1
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4
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564
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Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 3 months ago by 51k • written 3 months ago by • 0
0
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2
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315
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
3 months ago Gimena • 0
15
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23
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2.4k
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The difference when using Limma compare between 3 conditions vs 2 conditions
limma
3 months ago • updated 12 weeks ago Chris ▴ 20
2
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8
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690
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Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 4 months ago by 51k • written 4 months ago by • 0
5
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25
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1.3k
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 3 months ago by 51k • written 4 months ago by ▴ 10
7
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6
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614
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Batch Effect Correction, Gene Filtering
DGE limma
updated 4 months ago by 51k • written 4 months ago by • 0
0
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1
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350
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 4 months ago by 51k • written 4 months ago by • 0
0
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4
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527
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo limma hugene11stprobeset.db AffymetrixChip
4 months ago Efra • 0
5
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7
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653
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 4 months ago by 51k • written 4 months ago by • 0
2
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2
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369
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
4 months ago Sabiha ▴ 20
0
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2
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537
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
4 months ago kcarey • 0
1
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3
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547
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 5 months ago by • 0
2
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6
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762
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limma: vooma mean-variance trend and data filtration
MicroarrayData limma
4 months ago Lily Cheang ▴ 10
3
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8
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697
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Constrast for Time Course Experiments using Limma
limma
4 months ago dl17032000 • 0
8
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6
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668
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DGE analysis with LIMMA
limma
updated 4 months ago by 51k • written 4 months ago by • 0
0
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0
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242
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Can I combine collinear variables into a single value
BatchEffect limma
4 months ago Harrsha • 0
0
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3
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443
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Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 4 months ago by 51k • written 4 months ago by • 0
0
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4
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464
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
5 months ago • updated 4 months ago mperalc • 0
50 results • Page 1 of 1
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Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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