Showing : Regression • reset
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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
679
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 9 months ago by 68k • written 9 months ago by • 0
1
vote
3
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787
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
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2
replies
751
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 13 months ago by ▴ 10
0
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0
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558
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
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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 5.5 years ago by ▴ 10
0
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1
reply
788
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
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4
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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
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2
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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
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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
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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
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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
4.6k
views
Coping with a label/class imbalance in DESeq2
deseq2 rnaseq r regression
updated 8.6 years ago by 43k • written 8.6 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
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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
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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
11.1 years ago Michael Love 43k
0
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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
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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
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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 11.3 years ago by ▴ 280 • written 11.3 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
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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
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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
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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
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1.3k
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CAMDA 2013 Challenge: Big Data in Life Sciences
Sequencing Microarray Genetics Classification Clustering Regression Sequencing Microarray
12.2 years ago CAMDA 2013 ▴ 30
0
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10
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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
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2
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4.6k
views
edgeR choose the best model of GLM
Regression edgeR Regression edgeR
updated 12.2 years ago by 52k • written 12.2 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
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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
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lowess regression
Regression Regression
12.7 years ago Bogdan ▴ 670
1
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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
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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
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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
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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
13.5 years ago Ruppert Valentino ▴ 270
50 results • Page 1 of 1
Recent ...
Replies
Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr by Paul Harrison ▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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