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
486
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
616
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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
570
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
9 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 9 months ago by ▴ 10
0
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0
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480
views
multipollutant models
statistics Regression r limma
13 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 2.7 years ago by ▴ 30
1
vote
1
reply
1.0k
views
limma: pvalues for coefficients topTable
TimeSeriesExperiment Regression top limma
updated 3.4 years ago by 67k • written 3.4 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 4.2 years ago by ★ 5.2k • written 5.2 years ago by ▴ 10
0
votes
1
reply
718
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 4.9 years ago by 52k • written 4.9 years ago by • 0
1
vote
2
replies
997
views
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 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
3
votes
3
replies
1.4k
views
Limma - Two-color group differences *and* correlation with individual differences.
limma regression
updated 7.9 years ago by 52k • written 7.9 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 8.3 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 8.3 years ago by 43k • written 8.3 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 9.3 years ago by 43k • written 9.3 years ago by • 0
0
votes
1
reply
1.2k
views
GWASTools: quasi-/perfect linear separation
Regression
updated 10.3 years ago by ▴ 890 • 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 10.8 years ago by ★ 13k • written 10.8 years ago by ★ 13k
0
votes
1
reply
1.8k
views
Support vector regression
Classification Regression Classification Regression
updated 10.8 years ago by ★ 13k • written 10.8 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
10.8 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
votes
3
replies
9.2k
views
ggplot2 error
Regression Regression
10.9 years ago Alyaa Mahmoud ▴ 440
2
votes
5
replies
15k
views
Limma design and contrast matrix question.
Microarray Regression limma Microarray Regression limma
updated 10.9 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 11.0 years ago by ▴ 280 • written 11.0 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
replies
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
reply
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
11.1 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
replies
1.3k
views
CAMDA 2013 Challenge: Big Data in Life Sciences
Sequencing Microarray Genetics Classification Clustering Regression Sequencing Microarray
11.8 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
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4.4k
views
edgeR choose the best model of GLM
Regression edgeR Regression edgeR
updated 11.9 years ago by 52k • written 11.9 years ago by ▴ 40
0
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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 12.5 years ago by ▴ 130 • written 12.5 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 12.5 years ago by 25k • written 12.5 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
12.5 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
984
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
12.8 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 13.1 years ago by ▴ 60 • written 13.1 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
13.2 years ago Ruppert Valentino ▴ 270
50 results • Page 1 of 1
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Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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