Showing : regression • reset
2
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Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 8 months ago by 68k • written 8 months ago by ▴ 20
0
votes
3
replies
691
views
RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 9 months ago by 68k • written 9 months ago by • 0
1
vote
3
replies
798
views
Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression DESeq2
11 months ago • updated 9 months ago David W. H. • 0
0
votes
2
replies
764
views
WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
13 months ago w.cookson • 0
5
votes
25
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2.4k
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 13 months ago by 52k • written 14 months ago by ▴ 10
0
votes
0
replies
563
views
multipollutant models
statistics Regression r limma
17 months ago Jitendra ▴ 10
2
votes
4
replies
1.7k
views
Overfitting in limma
limma Regression overfitting
updated 3.0 years ago by 52k • written 3.0 years ago by ▴ 30
1
vote
1
reply
1.1k
views
limma: pvalues for coefficients topTable
TimeSeriesExperiment Regression top limma
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
4
votes
3
replies
1.4k
views
Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 4.5 years ago by ★ 5.2k • written 5.6 years ago by ▴ 10
0
votes
1
reply
790
views
Which Package Should I Use to Predict Model Output Using RNA Seq Data?
regression
updated 4.9 years ago by 52k • written 4.9 years ago by • 0
7
votes
4
replies
6.6k
views
Limma when to use zero intercept
limma regression differential expression linear model
updated 5.2 years ago by 52k • written 5.2 years ago by • 0
1
vote
2
replies
1.1k
views
EdgeR -- differentially expressed genes across a continuous variable
edger continuous regression
updated 6.3 years ago by 68k • written 6.3 years ago by • 0
6
votes
7
replies
2.7k
views
Multi-level experiment with limma
limma design and contrast matrix differential gene expression regression
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
3
votes
3
replies
1.5k
views
Limma - Two-color group differences *and* correlation with individual differences.
limma regression
updated 8.3 years ago by 52k • written 8.3 years ago by ▴ 30
1
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2
replies
4.0k
views
Kernel Ridge Regression in R for Drug-Target Interaction
regression kernel ridge r
updated 8.6 years ago by • 0 • written 9.1 years ago by • 0
2
votes
23
replies
4.7k
views
Coping with a label/class imbalance in DESeq2
deseq2 rnaseq r regression
updated 8.7 years ago by 43k • written 8.7 years ago by • 0
11
votes
3
replies
2.1k
views
Fit a multinomial to RNA-seq count data
voom limma glm multinomial regression
updated 8.8 years ago by ★ 3.4k • written 8.8 years ago by ▴ 110
1
vote
5
replies
2.1k
views
deseq2 normalized data
regression deseq2 counts
updated 9.7 years ago by 43k • written 9.7 years ago by • 0
0
votes
1
reply
1.3k
views
GWASTools: quasi-/perfect linear separation
Regression
updated 10.7 years ago by ▴ 890 • written 10.7 years ago by ★ 13k
0
votes
2
replies
2.4k
views
UCSC data anomaly in 50638 transcript(s): the cds cumulative length is
Genetics GO Regression Cancer TranscriptDb Genetics GO Regression Cancer TranscriptDb
updated 11.0 years ago by ▴ 570 • written 11.0 years ago by 16k
0
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1
reply
1.8k
views
Choosing the kernel for SVM (regression) using rminer package
Regression Regression
updated 11.1 years ago by ★ 13k • written 11.1 years ago by ★ 13k
0
votes
1
reply
1.9k
views
Support vector regression
Classification Regression Classification Regression
updated 11.1 years ago by ★ 13k • written 11.1 years ago by ★ 13k
0
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0
replies
1.7k
views
Data Analysis for Genomics, free HarvardX course, starts April 7
Regression Regression
11.2 years ago Michael Love 43k
0
votes
4
replies
2.7k
views
DESeq2 high fold change values for comparison of samples with zero counts
Regression DESeq DESeq2 Regression DESeq DESeq2
updated 11.3 years ago by 43k • written 11.3 years ago by ▴ 60
0
votes
3
replies
9.4k
views
ggplot2 error
Regression Regression
11.3 years ago Alyaa Mahmoud ▴ 440
2
votes
5
replies
16k
views
Limma design and contrast matrix question.
Microarray Regression limma Microarray Regression limma
updated 11.3 years ago by 68k • written 11.3 years ago by ▴ 380
0
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1
reply
1.9k
views
[MEDIPS] mergeFrames: `Error in rbind(output, cbind(chromosomes[i], new_start, new_stop)) `
Coverage Regression edgeR MEDIPS Coverage Regression edgeR MEDIPS
updated 11.4 years ago by ▴ 280 • written 11.4 years ago by ▴ 10
0
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2
replies
2.1k
views
[MEDIPS] Error in 1:max_signal_index : argument of length 0 - what does mean?
Preprocessing Regression MEDIPS Preprocessing Regression MEDIPS
updated 11.4 years ago by ▴ 570 • written 11.4 years ago by ▴ 20
0
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0
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2.0k
views
EdgeR Design matrix not of full rank. The following coefficients not estimable errorR
Regression edgeR Regression edgeR
11.4 years ago Gordon Smyth 52k
0
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0
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1.2k
views
EdgeR Design matrix not of full rank. The following coefficients not estimable errorR
Regression edgeR Regression edgeR
11.4 years ago Eugene Bolotin ▴ 20
0
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1
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1.9k
views
[R] freetype 2.5.2, problem with the survival package, build R 2.15.x with gcc 4.8.x
Regression Survival snpStats Regression Survival snpStats
11.4 years ago David Winsemius ▴ 40
0
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0
replies
3.9k
views
Inquiries about fitType on DESeq2
Regression DESeq2 Regression DESeq2
11.5 years ago Michael Love 43k
2
votes
2
replies
2.6k
views
[limma] [Rfit] [samr] Gene expression distribution using lmFit and eBayes
Microarray Regression Microarray Regression
updated 11.5 years ago by 52k • written 11.5 years ago by ▴ 30
0
votes
3
replies
4.2k
views
lower.limits and upper.limits in glmnet
Regression Regression
updated 11.6 years ago by ▴ 60 • written 11.6 years ago by ▴ 370
0
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0
replies
1.6k
views
CfP: CAMDA 2013 - 12th International Conference on Critical Assessment of Massive Data Analysis
Genetics Classification Regression Genetics Classification Regression
12.1 years ago CAMDA 2013 ▴ 30
0
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0
replies
1.3k
views
CAMDA 2013 Challenge: Big Data in Life Sciences
Sequencing Microarray Genetics Classification Clustering Regression Sequencing Microarray
12.2 years ago CAMDA 2013 ▴ 30
0
votes
10
replies
2.9k
views
assignChromosomeRegion in 2.6.0 ChIPpeakAnno
Microarray Annotation GO Network Regression Survival Infrastructure Escherichia coli ROC
12.2 years ago Julie Zhu ★ 4.3k
0
votes
2
replies
4.6k
views
edgeR choose the best model of GLM
Regression edgeR Regression edgeR
updated 12.2 years ago by 52k • written 12.3 years ago by ▴ 40
0
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7
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2.1k
views
affy code archeology: expresso behavior for liwong/invariantset
Regression gcrma Regression gcrma
updated 12.3 years ago by 68k • written 12.3 years ago by ★ 13k
0
votes
1
reply
1.2k
views
[R] lowess regression
Regression Regression
updated 12.7 years ago by ▴ 10 • written 12.7 years ago by ▴ 670
0
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0
replies
1.2k
views
lowess regression
Regression Regression
12.7 years ago Bogdan ▴ 670
1
vote
1
reply
7.4k
views
[LIMMA]lmFit with continuous predictor
Regression limma Regression limma
updated 12.9 years ago by ▴ 130 • written 12.9 years ago by ▴ 210
0
votes
3
replies
1.4k
views
edgeR and tagwise dispersion: overcorrection for multiple tests?
SAGE Regression edgeR BRAIN SAGE Regression edgeR BRAIN
updated 12.9 years ago by 25k • written 12.9 years ago by 52k
0
votes
0
replies
1.4k
views
edgeR and tagwise dispersion: overcorrection for multiple tests?
SAGE Regression edgeR BRAIN SAGE Regression edgeR BRAIN
12.9 years ago alessandro.guffanti@genomnia.com ▴ 330
0
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0
replies
1.3k
views
about edgeR
Regression Regression
12.9 years ago wang peter ★ 2.0k
0
votes
0
replies
1.6k
views
design and contrast matrix for limma time series without replicates
Microarray GO Regression limma Microarray GO Regression limma
13.0 years ago Chunxuan Shao ▴ 30
0
votes
0
replies
1.1k
views
Outcome~predictor model evaluation, repeated measurements
Regression Regression
13.0 years ago rad mac ▴ 10
0
votes
0
replies
1.9k
views
edgeR-DeSeq - inconsistency between Variance and Coefficient of Variation
Regression edgeR DESeq Regression edgeR DESeq
13.1 years ago Gordon Smyth 52k
8
votes
3
replies
7.8k
views
Removing batch effects with sva and combat using the sva package
Regression limma sva Regression limma sva
updated 13.4 years ago by ▴ 60 • written 13.4 years ago by ▴ 650
0
votes
0
replies
1.5k
views
Use of glm for multivariate logistic regression of microarray data
Microarray Regression Microarray Regression
13.6 years ago Ruppert Valentino ▴ 270
50 results • Page 1 of 1
Recent ...
Replies
Comment: parameters of filterByExpr by caroline.zanchi ▴ 10
It worked, I think I finally understand and accept that fact. Sorry and thank you again !
Comment: parameters of filterByExpr by Gordon Smyth 52k
You seem to be coming back to the same fixed (but incorrect) idea of what filterByExpr() should be doing. I have tried to explain that filt…
Answer: edgeR in DMR mode - replicates give batch effect - how to build design matrix wi by Gordon Smyth 52k
modelMatrixMeth() works correctly. The second replicate factor has not been lost. Please do not make ad hoc manual modifications to the de…
Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k
Probably not. Any given gene may be appended with many different GO terms, so you would end up with something that is not very useful. ``…
Comment: Heatmap of rnaseq data with z-score scale by James W. MacDonald 68k
`heatmap.2` is a CRAN package, and that's the relevant issue for this plot. It's got nothing to do with `DESeq2` or any other Bioconductor …
Votes
Answer: LogFC values in edgeR - w/wo intercept
How to formulate 2 factor nested design in DESeq2
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
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