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27
votes
7
replies
12k
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Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 14 months ago by ▴ 10 • written 7.1 years ago by ▴ 40
19
votes
4
replies
8.8k
views
Confidence intervals on edgeR logFC
edgeR statistics confidence interval
updated 8.7 years ago by • 0 • written 10.2 years ago by ▴ 40
10
votes
14
replies
14k
views
how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 3.7 years ago by ▴ 20 • written 8.8 years ago by ▴ 30
8
votes
3
replies
3.6k
views
Differing topTable() results with Limma with and without specifying coefficient
limma microarray statistics
updated 8.6 years ago by 52k • written 8.6 years ago by • 0
8
votes
8
replies
7.7k
views
Voom transformation from counts and normalization to negative values
rnaseq voom limma tcga statistics
updated 6.2 years ago by ★ 7.9k • written 6.2 years ago by ▴ 60
3
votes
5
replies
1.5k
views
P adjusted values in Deseq2
DESeq2 Statistics
written 3.9 years ago by • 0
3
votes
0
replies
2.4k
views
Job: Postdoctoral Scientist, Statistical Bioinformatics and Proteomics, WEHI Australia
job proteomics Job statistics
5.1 years ago • updated 4.9 years ago Gordon Smyth 52k
3
votes
3
replies
1.7k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2 apeglm statistics
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
2
votes
2
replies
3.7k
views
How adjusted p-values are calculated in limma
limma r transcriptomics FDR statistics
updated 5.2 years ago by 52k • written 5.2 years ago by ▴ 10
2
votes
2
replies
1.2k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 7 months ago by • 0 • written 8.5 years ago by • 0
2
votes
3
replies
1.7k
views
RNAseq outlier is a critical sample
rnaseq outlier statistics batch effect
updated 8.5 years ago by 52k • written 8.5 years ago by • 0
2
votes
2
replies
8.4k
views
edgeR: How is FDR calculated for logFC? (False Discovery Rate)
edgeR bioconductor fdr statistics differential gene expression
8.0 years ago jol.espinoz ▴ 40
2
votes
4
replies
1.4k
views
Removing batch effect on edgeR when interactons are looked at
rnaseq edger statistics model matrix
updated 7.2 years ago by ★ 13k • written 7.2 years ago by ▴ 90
2
votes
0
replies
1.0k
views
Job: Multiple open positions in biomedical statistics at Eurac Research, Italy
epidemiology statistics bioinformatics Job
4.2 years ago Johannes Rainer ★ 2.1k
1
vote
0
replies
951
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Job: Lecturer in Statistics - School of Mathematics and Statistics - University of St Andrews
computational teaching statistics research
2.4 years ago Andy Lynch ▴ 120
1
vote
0
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1.7k
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Job: PhD Positions in Computational Cancer Research
computational biology image analysis cancer genomics statistics Job
8.0 years ago Bernd Fischer ▴ 550
1
vote
2
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2.9k
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the statistical test that DESeq2 use
deseq2 statistics
updated 7.8 years ago by ★ 7.9k • written 7.8 years ago by • 0
1
vote
1
reply
2.3k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 19 months ago by ★ 4.6k • written 19 months ago by ▴ 10
1
vote
0
replies
1.4k
views
Job: Statistical Research Associate
biostatistics statistics sas git assay Job
6.6 years ago Fred Hutch (Recruiting) ▴ 40
1
vote
4
replies
1.4k
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Do the gene set statistics of the ROAST paper correspond to those implemented in the .roastEffects R function?
limma roast statistics source code gene set testing
6.3 years ago Andrea Carenzo • 0
1
vote
2
replies
1.1k
views
What to do with microarray probes that catch multiple genes?
affymetrix microarrays microarray probe statistics
updated 6.3 years ago by 67k • written 6.3 years ago by • 0
1
vote
2
replies
1.1k
views
Newbie to all of this
bioconductor statistics
6.1 years ago sportwoo • 0
1
vote
6
replies
3.1k
views
DESeq2 unbalanced sample size
deseq2 bioconductor bioinformatics statistics
updated 21 months ago by 43k • written 6.0 years ago by • 0
1
vote
0
replies
2.2k
views
Job: Postdoctoral Research Fellow in Bioinformatics - Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Mainz, Germany
bioinformatician job rnaseq statistics systemsbiology Job
9.6 years ago Federico Marini ▴ 180
1
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2
replies
2.2k
views
how to perform pre ranked GSEA in R?
r microarray statistics GSEA
updated 7.7 years ago by • 0 • written 9.8 years ago by ▴ 80
1
vote
0
replies
1.1k
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Job: Post-Doctoral Research Fellow, Cancer Genomics
genomics seattle bioinformatics data science statistics Job
4.5 years ago Fred Hutch (Recruiting) ▴ 40
1
vote
2
replies
1.3k
views
Re-calculation of Padj (P adjusted value)
statistics Benjamini–Hochberg procedure deseq2
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 60
1
vote
0
replies
1.9k
views
News: Workshop Statistical Methods for Post Genomic Data in Munich, February 12-13, 2015
statistics workshop news News
10.2 years ago gagneur ▴ 10
1
vote
1
reply
547
views
Further analysis after limma regression output
statistics Epigenetics limma
updated 14 months ago by 67k • written 14 months ago by ▴ 10
1
vote
0
replies
862
views
Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
2.3 years ago arisarkar88 ▴ 40
1
vote
0
replies
990
views
Job: Research Fellow in Prostate Cancer Proteomics (Bioinformatics/Stats/Data Analysis) - University of St Andrews
Multiomics Proteomics Cancer Statistics Bioinformatics
2.4 years ago Andy Lynch ▴ 120
0
votes
2
replies
1.3k
views
comparing two GOstats result lists
gostats statistics
updated 6.5 years ago by 67k • written 6.5 years ago by ▴ 30
0
votes
0
replies
2.1k
views
Job: Postdoc and PhD student in Bioinformatics/Biostatistics
genomics NGS R genetics statistics
6.4 years ago • updated 4.0 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
1.1k
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Job: Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
singlecellRNA-Seq pathview statistics R
3.7 years ago • updated 3.6 years ago Luo Weijun ★ 1.6k
0
votes
3
replies
1.8k
views
Reading large file (15GB) in R
R Rstudio Bioconducter statistics
updated 2.8 years ago by 21k • written 2.9 years ago by ▴ 10
0
votes
0
replies
1.6k
views
Job: Come apply for our Epidemiologist, AncestryHealth role
genomics genetics design statistics scientist Job
9.4 years ago careers • 0
0
votes
2
replies
1.2k
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News: Ascona Workshop “Biological systems: from first principles to data-​driven modelling and back” 27. 3. - 1. 4. 2022
theory modeling statistics ascona Workshop
3.1 years ago • updated 22 months ago Wolfgang Huber ★ 13k
0
votes
3
replies
1.5k
views
batch effect in EPIC array data
statistics Epigenetics R
updated 21 months ago by ▴ 760 • written 21 months ago by ▴ 10
0
votes
0
replies
924
views
package for mismatch distribution?
genetics statistics
5.9 years ago myriam.croze07 • 0
0
votes
1
reply
1.1k
views
Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS GWAS resampling resample statistics
5.8 years ago naglemi ▴ 10
0
votes
0
replies
1.5k
views
Job: Postdoc and PhD student in Bioinformatics/Biostatistics
NGS R statistics genomics big data Job
5.8 years ago • updated 5.0 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
833
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Job: PhD position in Bioinformatics in Jena
Statistics ComputationalBiology Aging MachineLearning
23 months ago alena.vanboemmel • 0
0
votes
0
replies
1.2k
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
5.3 years ago tatabox • 0
0
votes
0
replies
453
views
Job: Statistics Lectureships at St Andrews
JobPosting computational statistics
9 months ago Andy Lynch ▴ 120
0
votes
1
reply
925
views
Exclude interaction terms from the design
deseq2 statistics modelling
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
votes
0
replies
2.1k
views
Job: Full position as Statistician at ETH Zurich in Personalized Medicine Consultancy/Data Analysis
statistics consultancy personalized medicine Job
10.1 years ago Daniel Stekhoven ▴ 10
0
votes
1
reply
969
views
How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression
5.1 years ago A • 0
0
votes
4
replies
3.1k
views
XCMS for targeted metabolomic/lipidomics/proteomics
xcms metabolomics lipidomics statistics
8.9 years ago Titan • 0
0
votes
0
replies
898
views
Job: Two Bioinformatics Fellowship Positions at US EPA
bioinformatics toxicology Job sequenicng statistics
4.4 years ago • updated 4.1 years ago whduke • 0
0
votes
1
reply
529
views
DEseq2 : Complex design with a mixture of male and female mice
statistics DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
50 results • Page 1 of 1
Recent ...
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Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable by Gordon Smyth 52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd by liu.n • 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0
> dim(spe) [1] 19962 425
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Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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