Showing : regression • reset
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
27 days ago • updated 22 days ago w.cookson • 0
5
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25
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814
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limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 20 days ago by 50k • written 4 weeks ago by ▴ 10
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216
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multipollutant models
statistics Regression r limma
4 months ago Jitendra ▴ 10
2
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4
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1.1k
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Overfitting in limma
limma Regression overfitting
updated 23 months ago by 50k • written 24 months ago by ▴ 30
1
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1
reply
797
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limma: pvalues for coefficients topTable
TimeSeriesExperiment Regression top limma
updated 2.7 years ago by 65k • written 2.7 years ago by • 0
4
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3
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987
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Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 3.5 years ago by ★ 5.1k • written 4.5 years ago by ▴ 10
0
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1
reply
559
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Which Package Should I Use to Predict Model Output Using RNA Seq Data?
regression
updated 3.8 years ago by 50k • written 3.8 years ago by • 0
7
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4
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4.1k
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Limma when to use zero intercept
limma regression differential expression linear model
updated 4.2 years ago by 50k • written 4.2 years ago by • 0
1
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2
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778
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EdgeR -- differentially expressed genes across a continuous variable
edger continuous regression
updated 5.2 years ago by 65k • written 5.2 years ago by • 0
6
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7
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2.1k
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Multi-level experiment with limma
limma design and contrast matrix differential gene expression regression
updated 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
3
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3
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1.2k
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Limma - Two-color group differences *and* correlation with individual differences.
limma regression
updated 7.2 years ago by 50k • written 7.2 years ago by ▴ 30
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2
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3.4k
views
Kernel Ridge Regression in R for Drug-Target Interaction
regression kernel ridge r
updated 7.6 years ago by • 0 • written 8.0 years ago by • 0
2
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23
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3.5k
views
Coping with a label/class imbalance in DESeq2
deseq2 rnaseq r regression
updated 7.6 years ago by 41k • written 7.6 years ago by • 0
11
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3
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1.7k
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Fit a multinomial to RNA-seq count data
voom limma glm multinomial regression
updated 7.8 years ago by ★ 3.3k • written 7.8 years ago by ▴ 110
1
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5
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1.8k
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deseq2 normalized data
regression deseq2 counts
updated 8.6 years ago by 41k • written 8.6 years ago by • 0
0
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1
reply
993
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GWASTools: quasi-/perfect linear separation
Regression
updated 9.6 years ago by ▴ 870 • written 9.6 years ago by ★ 13k
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2
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2.0k
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UCSC data anomaly in 50638 transcript(s): the cds cumulative length is
Genetics GO Regression Cancer TranscriptDb Genetics GO Regression Cancer TranscriptDb
updated 9.9 years ago by ▴ 570 • written 9.9 years ago by 16k
0
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1
reply
1.5k
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Choosing the kernel for SVM (regression) using rminer package
Regression Regression
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ★ 13k
0
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1
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1.5k
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Support vector regression
Classification Regression Classification Regression
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ★ 13k
0
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0
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1.5k
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Data Analysis for Genomics, free HarvardX course, starts April 7
Regression Regression
10.1 years ago Michael Love 41k
0
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4
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2.5k
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DESeq2 high fold change values for comparison of samples with zero counts
Regression DESeq DESeq2 Regression DESeq DESeq2
updated 10.2 years ago by 41k • written 10.2 years ago by ▴ 60
0
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3
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8.9k
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ggplot2 error
Regression Regression
10.2 years ago Alyaa Mahmoud ▴ 440
2
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5
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15k
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Limma design and contrast matrix question.
Microarray Regression limma Microarray Regression limma
updated 10.3 years ago by 65k • written 10.3 years ago by ▴ 350
0
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1
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1.6k
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[MEDIPS] mergeFrames: `Error in rbind(output, cbind(chromosomes[i], new_start, new_stop)) `
Coverage Regression edgeR MEDIPS Coverage Regression edgeR MEDIPS
updated 10.3 years ago by ▴ 240 • written 10.3 years ago by ▴ 10
0
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2
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1.8k
views
[MEDIPS] Error in 1:max_signal_index : argument of length 0 - what does mean?
Preprocessing Regression MEDIPS Preprocessing Regression MEDIPS
updated 10.3 years ago by ▴ 570 • written 10.3 years ago by ▴ 20
0
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0
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1.7k
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EdgeR Design matrix not of full rank. The following coefficients not estimable errorR
Regression edgeR Regression edgeR
10.3 years ago Gordon Smyth 50k
0
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0
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968
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EdgeR Design matrix not of full rank. The following coefficients not estimable errorR
Regression edgeR Regression edgeR
10.3 years ago Eugene Bolotin ▴ 20
0
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1
reply
1.6k
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
10.4 years ago David Winsemius ▴ 40
0
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0
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3.5k
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Inquiries about fitType on DESeq2
Regression DESeq2 Regression DESeq2
10.4 years ago Michael Love 41k
2
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2
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2.2k
views
[limma] [Rfit] [samr] Gene expression distribution using lmFit and eBayes
Microarray Regression Microarray Regression
updated 10.4 years ago by 50k • written 10.4 years ago by ▴ 30
0
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3
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3.6k
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lower.limits and upper.limits in glmnet
Regression Regression
updated 10.5 years ago by ▴ 60 • written 10.5 years ago by ▴ 370
0
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0
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1.4k
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CfP: CAMDA 2013 - 12th International Conference on Critical Assessment of Massive Data Analysis
Genetics Classification Regression Genetics Classification Regression
11.0 years ago CAMDA 2013 ▴ 30
0
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0
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1.1k
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CAMDA 2013 Challenge: Big Data in Life Sciences
Sequencing Microarray Genetics Classification Clustering Regression Sequencing Microarray
11.1 years ago CAMDA 2013 ▴ 30
0
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10
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2.4k
views
assignChromosomeRegion in 2.6.0 ChIPpeakAnno
Microarray Annotation GO Network Regression Survival Infrastructure Escherichia coli ROC
11.1 years ago Julie Zhu ★ 4.3k
0
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2
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4.2k
views
edgeR choose the best model of GLM
Regression edgeR Regression edgeR
updated 11.2 years ago by 50k • written 11.2 years ago by ▴ 40
0
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7
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1.7k
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affy code archeology: expresso behavior for liwong/invariantset
Regression gcrma Regression gcrma
updated 11.2 years ago by 65k • written 11.3 years ago by ★ 13k
0
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1
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993
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[R] lowess regression
Regression Regression
updated 11.6 years ago by ▴ 10 • written 11.6 years ago by ▴ 670
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0
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1.0k
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lowess regression
Regression Regression
11.6 years ago Bogdan ▴ 670
1
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1
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7.1k
views
[LIMMA]lmFit with continuous predictor
Regression limma Regression limma
updated 11.8 years ago by ▴ 130 • written 11.8 years ago by ▴ 210
0
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3
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1.2k
views
edgeR and tagwise dispersion: overcorrection for multiple tests?
SAGE Regression edgeR BRAIN SAGE Regression edgeR BRAIN
updated 11.8 years ago by 25k • written 11.8 years ago by 50k
0
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0
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1.2k
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edgeR and tagwise dispersion: overcorrection for multiple tests?
SAGE Regression edgeR BRAIN SAGE Regression edgeR BRAIN
11.8 years ago alessandro.guffanti@genomnia.com ▴ 330
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0
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1.1k
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about edgeR
Regression Regression
11.8 years ago wang peter ★ 2.0k
0
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0
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1.5k
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design and contrast matrix for limma time series without replicates
Microarray GO Regression limma Microarray GO Regression limma
11.9 years ago Chunxuan Shao ▴ 30
0
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0
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827
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Outcome~predictor model evaluation, repeated measurements
Regression Regression
12.0 years ago rad mac ▴ 10
0
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0
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1.7k
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edgeR-DeSeq - inconsistency between Variance and Coefficient of Variation
Regression edgeR DESeq Regression edgeR DESeq
12.1 years ago Gordon Smyth 50k
8
votes
3
replies
6.9k
views
Removing batch effects with sva and combat using the sva package
Regression limma sva Regression limma sva
updated 12.4 years ago by ▴ 60 • written 12.4 years ago by ▴ 650
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0
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1.2k
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Use of glm for multivariate logistic regression of microarray data
Microarray Regression Microarray Regression
12.5 years ago Ruppert Valentino ▴ 270
0
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0
replies
748
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Binomial regression of HTqPCR data
Regression HTqPCR Regression HTqPCR
12.5 years ago Christopher Howerton ▴ 40
0
votes
0
replies
896
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Regression analysis using expression microarray to determine phenotypic correlation
Microarray Regression Microarray Regression
12.5 years ago Ruppert Valentino ▴ 270
0
votes
6
replies
1.4k
views
SNPcounts error in SNPlocs.Hsapiens.dbSNP.20110815_0.99.3 (i.e., my attempt to update SNPlocs to dbSNP build 134)
Regression SNPlocs Biostrings Regression SNPlocs Biostrings
updated 12.6 years ago by 6.7k • written 12.6 years ago by ★ 4.2k
50 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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