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 3 months ago by 67k • written 3 months ago by ▴ 10
0
votes
3
replies
468
views
RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 4 months ago by 67k • written 4 months ago by • 0
1
vote
3
replies
601
views
Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression DESeq2
6 months ago • updated 4 months ago David W. H. • 0
0
votes
2
replies
560
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
8 months ago w.cookson • 0
5
votes
25
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1.8k
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 8 months ago by 52k • written 8 months ago by ▴ 10
0
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0
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475
views
multipollutant models
statistics Regression r limma
12 months ago Jitendra ▴ 10
2
votes
4
replies
1.5k
views
Overfitting in limma
limma Regression overfitting
updated 2.6 years ago by 52k • written 2.6 years ago by ▴ 30
1
vote
1
reply
1.0k
views
limma: pvalues for coefficients topTable
TimeSeriesExperiment Regression top limma
updated 3.3 years ago by 67k • written 3.3 years ago by • 0
4
votes
3
replies
1.2k
views
Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 4.1 years ago by ★ 5.2k • written 5.1 years ago by ▴ 10
0
votes
1
reply
716
views
Which Package Should I Use to Predict Model Output Using RNA Seq Data?
regression
updated 4.5 years ago by 52k • written 4.5 years ago by • 0
7
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4
replies
5.6k
views
Limma when to use zero intercept
limma regression differential expression linear model
updated 4.8 years ago by 52k • written 4.8 years ago by • 0
1
vote
2
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991
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EdgeR -- differentially expressed genes across a continuous variable
edger continuous regression
updated 5.9 years ago by 67k • written 5.9 years ago by • 0
6
votes
7
replies
2.5k
views
Multi-level experiment with limma
limma design and contrast matrix differential gene expression regression
updated 7.4 years ago by ★ 28k • written 7.4 years ago by • 0
3
votes
3
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1.4k
views
Limma - Two-color group differences *and* correlation with individual differences.
limma regression
updated 7.9 years ago by 52k • written 7.9 years ago by ▴ 30
1
vote
2
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3.8k
views
Kernel Ridge Regression in R for Drug-Target Interaction
regression kernel ridge r
updated 8.2 years ago by • 0 • written 8.7 years ago by • 0
2
votes
23
replies
4.2k
views
Coping with a label/class imbalance in DESeq2
deseq2 rnaseq r regression
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
11
votes
3
replies
2.0k
views
Fit a multinomial to RNA-seq count data
voom limma glm multinomial regression
updated 8.4 years ago by ★ 3.4k • written 8.4 years ago by ▴ 110
1
vote
5
replies
2.0k
views
deseq2 normalized data
regression deseq2 counts
updated 9.2 years ago by 43k • written 9.2 years ago by • 0
0
votes
1
reply
1.2k
views
GWASTools: quasi-/perfect linear separation
Regression
updated 10.3 years ago by ▴ 870 • written 10.3 years ago by ★ 13k
0
votes
2
replies
2.3k
views
UCSC data anomaly in 50638 transcript(s): the cds cumulative length is
Genetics GO Regression Cancer TranscriptDb Genetics GO Regression Cancer TranscriptDb
updated 10.6 years ago by ▴ 570 • written 10.6 years ago by 16k
0
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1
reply
1.7k
views
Choosing the kernel for SVM (regression) using rminer package
Regression Regression
updated 10.7 years ago by ★ 13k • written 10.7 years ago by ★ 13k
0
votes
1
reply
1.7k
views
Support vector regression
Classification Regression Classification Regression
updated 10.7 years ago by ★ 13k • written 10.7 years ago by ★ 13k
0
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0
replies
1.6k
views
Data Analysis for Genomics, free HarvardX course, starts April 7
Regression Regression
10.7 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 10.9 years ago by 43k • written 10.9 years ago by ▴ 60
0
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3
replies
9.2k
views
ggplot2 error
Regression Regression
10.9 years ago Alyaa Mahmoud ▴ 440
2
votes
5
replies
15k
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Limma design and contrast matrix question.
Microarray Regression limma Microarray Regression limma
updated 10.9 years ago by 67k • written 10.9 years ago by ▴ 380
0
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1
reply
1.8k
views
[MEDIPS] mergeFrames: `Error in rbind(output, cbind(chromosomes[i], new_start, new_stop)) `
Coverage Regression edgeR MEDIPS Coverage Regression edgeR MEDIPS
updated 10.9 years ago by ▴ 280 • written 10.9 years ago by ▴ 10
0
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2
replies
2.0k
views
[MEDIPS] Error in 1:max_signal_index : argument of length 0 - what does mean?
Preprocessing Regression MEDIPS Preprocessing Regression MEDIPS
updated 11.0 years ago by ▴ 570 • written 11.0 years ago by ▴ 20
0
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0
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1.9k
views
EdgeR Design matrix not of full rank. The following coefficients not estimable errorR
Regression edgeR Regression edgeR
11.0 years ago Gordon Smyth 52k
0
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0
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1.1k
views
EdgeR Design matrix not of full rank. The following coefficients not estimable errorR
Regression edgeR Regression edgeR
11.0 years ago Eugene Bolotin ▴ 20
0
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1
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1.8k
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
11.0 years ago David Winsemius ▴ 40
0
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0
replies
3.8k
views
Inquiries about fitType on DESeq2
Regression DESeq2 Regression DESeq2
11.1 years ago Michael Love 43k
2
votes
2
replies
2.4k
views
[limma] [Rfit] [samr] Gene expression distribution using lmFit and eBayes
Microarray Regression Microarray Regression
updated 11.1 years ago by 52k • written 11.1 years ago by ▴ 30
0
votes
3
replies
4.0k
views
lower.limits and upper.limits in glmnet
Regression Regression
updated 11.2 years ago by ▴ 60 • written 11.2 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
11.7 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
11.7 years ago CAMDA 2013 ▴ 30
0
votes
10
replies
2.7k
views
assignChromosomeRegion in 2.6.0 ChIPpeakAnno
Microarray Annotation GO Network Regression Survival Infrastructure Escherichia coli ROC
11.8 years ago Julie Zhu ★ 4.3k
0
votes
2
replies
4.4k
views
edgeR choose the best model of GLM
Regression edgeR Regression edgeR
updated 11.8 years ago by 52k • written 11.8 years ago by ▴ 40
0
votes
7
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1.9k
views
affy code archeology: expresso behavior for liwong/invariantset
Regression gcrma Regression gcrma
updated 11.9 years ago by 67k • written 11.9 years ago by ★ 13k
0
votes
1
reply
1.2k
views
[R] lowess regression
Regression Regression
updated 12.3 years ago by ▴ 10 • written 12.3 years ago by ▴ 670
0
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0
replies
1.1k
views
lowess regression
Regression Regression
12.3 years ago Bogdan ▴ 670
1
vote
1
reply
7.3k
views
[LIMMA]lmFit with continuous predictor
Regression limma Regression limma
updated 12.4 years ago by ▴ 130 • written 12.4 years ago by ▴ 210
0
votes
3
replies
1.3k
views
edgeR and tagwise dispersion: overcorrection for multiple tests?
SAGE Regression edgeR BRAIN SAGE Regression edgeR BRAIN
updated 12.4 years ago by 25k • written 12.4 years ago by 52k
0
votes
0
replies
1.3k
views
edgeR and tagwise dispersion: overcorrection for multiple tests?
SAGE Regression edgeR BRAIN SAGE Regression edgeR BRAIN
12.4 years ago alessandro.guffanti@genomnia.com ▴ 330
0
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0
replies
1.2k
views
about edgeR
Regression Regression
12.5 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
12.6 years ago Chunxuan Shao ▴ 30
0
votes
0
replies
980
views
Outcome~predictor model evaluation, repeated measurements
Regression Regression
12.6 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
12.7 years ago Gordon Smyth 52k
8
votes
3
replies
7.5k
views
Removing batch effects with sva and combat using the sva package
Regression limma sva Regression limma sva
updated 13.0 years ago by ▴ 60 • written 13.0 years ago by ▴ 650
0
votes
0
replies
1.4k
views
Use of glm for multivariate logistic regression of microarray data
Microarray Regression Microarray Regression
13.1 years ago Ruppert Valentino ▴ 270
50 results • Page 1 of 1
Recent ...
Replies
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200
Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k
Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…
Votes
Answer: nightmare to make custom txdb for genomes from ToxoDB
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
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