Showing : Regression • reset
2
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311
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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 7 weeks ago by 67k • written 7 weeks ago by ▴ 10
0
votes
3
replies
424
views
RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 3 months ago by 67k • written 3 months ago by • 0
1
vote
3
replies
547
views
Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression DESeq2
4 months ago • updated 3 months ago David W. H. • 0
0
votes
2
replies
526
views
WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
7 months ago w.cookson • 0
5
votes
25
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1.7k
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 7 months ago by 51k • written 7 months ago by ▴ 10
0
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0
replies
452
views
multipollutant models
statistics Regression r limma
11 months ago Jitendra ▴ 10
2
votes
4
replies
1.4k
views
Overfitting in limma
limma Regression overfitting
updated 2.5 years ago by 51k • written 2.5 years ago by ▴ 30
1
vote
1
reply
995
views
limma: pvalues for coefficients topTable
TimeSeriesExperiment Regression top limma
updated 3.2 years ago by 67k • written 3.2 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 4.0 years ago by ★ 5.2k • written 5.0 years ago by ▴ 10
0
votes
1
reply
691
views
Which Package Should I Use to Predict Model Output Using RNA Seq Data?
regression
updated 4.3 years ago by 51k • written 4.4 years ago by • 0
7
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4
replies
5.3k
views
Limma when to use zero intercept
limma regression differential expression linear model
updated 4.7 years ago by 51k • written 4.7 years ago by • 0
1
vote
2
replies
966
views
EdgeR -- differentially expressed genes across a continuous variable
edger continuous regression
updated 5.8 years ago by 67k • written 5.8 years ago by • 0
6
votes
7
replies
2.4k
views
Multi-level experiment with limma
limma design and contrast matrix differential gene expression regression
updated 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
3
votes
3
replies
1.4k
views
Limma - Two-color group differences *and* correlation with individual differences.
limma regression
updated 7.8 years ago by 51k • written 7.8 years ago by ▴ 30
1
vote
2
replies
3.8k
views
Kernel Ridge Regression in R for Drug-Target Interaction
regression kernel ridge r
updated 8.1 years ago by • 0 • written 8.5 years ago by • 0
2
votes
23
replies
4.1k
views
Coping with a label/class imbalance in DESeq2
deseq2 rnaseq r regression
updated 8.1 years ago by 42k • written 8.1 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 8.3 years ago by ★ 3.4k • written 8.3 years ago by ▴ 110
1
vote
5
replies
2.0k
views
deseq2 normalized data
regression deseq2 counts
updated 9.1 years ago by 42k • written 9.1 years ago by • 0
0
votes
1
reply
1.1k
views
GWASTools: quasi-/perfect linear separation
Regression
updated 10.2 years ago by ▴ 870 • written 10.2 years ago by ★ 13k
0
votes
2
replies
2.2k
views
UCSC data anomaly in 50638 transcript(s): the cds cumulative length is
Genetics GO Regression Cancer TranscriptDb Genetics GO Regression Cancer TranscriptDb
updated 10.5 years ago by ▴ 570 • written 10.5 years ago by 16k
0
votes
1
reply
1.7k
views
Choosing the kernel for SVM (regression) using rminer package
Regression Regression
updated 10.6 years ago by ★ 13k • written 10.6 years ago by ★ 13k
0
votes
1
reply
1.7k
views
Support vector regression
Classification Regression Classification Regression
updated 10.6 years ago by ★ 13k • written 10.6 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
10.6 years ago Michael Love 42k
0
votes
4
replies
2.6k
views
DESeq2 high fold change values for comparison of samples with zero counts
Regression DESeq DESeq2 Regression DESeq DESeq2
updated 10.8 years ago by 42k • written 10.8 years ago by ▴ 60
0
votes
3
replies
9.1k
views
ggplot2 error
Regression Regression
10.8 years ago Alyaa Mahmoud ▴ 440
2
votes
5
replies
15k
views
Limma design and contrast matrix question.
Microarray Regression limma Microarray Regression limma
updated 10.8 years ago by 67k • written 10.8 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 10.8 years ago by ▴ 280 • written 10.8 years ago by ▴ 10
0
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2
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2.0k
views
[MEDIPS] Error in 1:max_signal_index : argument of length 0 - what does mean?
Preprocessing Regression MEDIPS Preprocessing Regression MEDIPS
updated 10.8 years ago by ▴ 570 • written 10.8 years ago by ▴ 20
0
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0
replies
1.8k
views
EdgeR Design matrix not of full rank. The following coefficients not estimable errorR
Regression edgeR Regression edgeR
10.9 years ago Gordon Smyth 51k
0
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0
replies
1.1k
views
EdgeR Design matrix not of full rank. The following coefficients not estimable errorR
Regression edgeR Regression edgeR
10.9 years ago Eugene Bolotin ▴ 20
0
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1
reply
1.7k
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
10.9 years ago David Winsemius ▴ 40
0
votes
0
replies
3.8k
views
Inquiries about fitType on DESeq2
Regression DESeq2 Regression DESeq2
11.0 years ago Michael Love 42k
2
votes
2
replies
2.4k
views
[limma] [Rfit] [samr] Gene expression distribution using lmFit and eBayes
Microarray Regression Microarray Regression
updated 11.0 years ago by 51k • written 11.0 years ago by ▴ 30
0
votes
3
replies
3.9k
views
lower.limits and upper.limits in glmnet
Regression Regression
updated 11.1 years ago by ▴ 60 • written 11.1 years ago by ▴ 370
0
votes
0
replies
1.5k
views
CfP: CAMDA 2013 - 12th International Conference on Critical Assessment of Massive Data Analysis
Genetics Classification Regression Genetics Classification Regression
11.6 years ago CAMDA 2013 ▴ 30
0
votes
0
replies
1.3k
views
CAMDA 2013 Challenge: Big Data in Life Sciences
Sequencing Microarray Genetics Classification Clustering Regression Sequencing Microarray
11.6 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
11.7 years ago • updated 11.6 years ago Julie Zhu ★ 4.3k
0
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2
replies
4.4k
views
edgeR choose the best model of GLM
Regression edgeR Regression edgeR
updated 11.7 years ago by 51k • written 11.7 years ago by ▴ 40
0
votes
7
replies
1.9k
views
affy code archeology: expresso behavior for liwong/invariantset
Regression gcrma Regression gcrma
updated 11.8 years ago by 67k • written 11.8 years ago by ★ 13k
0
votes
1
reply
1.2k
views
[R] lowess regression
Regression Regression
updated 12.2 years ago by ▴ 10 • written 12.2 years ago by ▴ 670
0
votes
0
replies
1.1k
views
lowess regression
Regression Regression
12.2 years ago Bogdan ▴ 670
1
vote
1
reply
7.3k
views
[LIMMA]lmFit with continuous predictor
Regression limma Regression limma
updated 12.3 years ago by ▴ 130 • written 12.3 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 12.3 years ago by 25k • written 12.3 years ago by 51k
0
votes
0
replies
1.3k
views
edgeR and tagwise dispersion: overcorrection for multiple tests?
SAGE Regression edgeR BRAIN SAGE Regression edgeR BRAIN
12.3 years ago alessandro.guffanti@genomnia.com ▴ 330
0
votes
0
replies
1.2k
views
about edgeR
Regression Regression
12.4 years ago wang peter ★ 2.0k
0
votes
0
replies
1.5k
views
design and contrast matrix for limma time series without replicates
Microarray GO Regression limma Microarray GO Regression limma
12.5 years ago Chunxuan Shao ▴ 30
0
votes
0
replies
956
views
Outcome~predictor model evaluation, repeated measurements
Regression Regression
12.5 years ago rad mac ▴ 10
0
votes
0
replies
1.8k
views
edgeR-DeSeq - inconsistency between Variance and Coefficient of Variation
Regression edgeR DESeq Regression edgeR DESeq
12.6 years ago Gordon Smyth 51k
8
votes
3
replies
7.4k
views
Removing batch effects with sva and combat using the sva package
Regression limma sva Regression limma sva
updated 12.9 years ago by ▴ 60 • written 12.9 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
13.0 years ago Ruppert Valentino ▴ 270
50 results • Page 1 of 1
Recent ...
Replies
Comment: Differential Expression Analysis with unbalanced batches without replication bet by Thili • 0
Thank you for your reply. I currently have batch-corrected data processed with scvi-tools (specifically, totalvi) and have followed the sam…
Comment: Problem at champ.load by andrew.gibbons • 0
I'd love to know if anyone has a workaround too. I've tried rolling back ChAMP and R to the previous versions that others have said work wi…
Comment: ESTMATE, MCPcounter, EPIC, xCell input by Kang • 0
These are not, as far as I know, bioconductor packages. You should query on the websites for those specific software programs. @[mapquest][…
Comment: Robust way of dealing with low number of samples for Differential Gene Expressio by Kang • 0
I believe that pseudo-bulking is a strong way to approach DE, as long as it is possible to reliably identify the cell type across data and …
Comment: GOstats kegg analysis in wheat - help - none of the objects in the first column by GV Yoshikawa • 0
Thank you for the reply. I tried swapping columns before asking, it made no difference. head(keggframeData) path_id kegg…
Votes
A: Up/Down Regulated GeneList from edgeR and R
A: Up/Down Regulated GeneList from edgeR and R
A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
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