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25
votes
7
replies
10k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 6 months ago by ▴ 10 • written 6.5 years ago by ▴ 30
19
votes
4
replies
8.1k
views
Confidence intervals on edgeR logFC
edgeR statistics confidence interval
updated 8.0 years ago by • 0 • written 9.6 years ago by ▴ 40
10
votes
14
replies
13k
views
how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 3.1 years ago by ▴ 20 • written 8.2 years ago by ▴ 30
8
votes
3
replies
3.2k
views
Differing topTable() results with Limma with and without specifying coefficient
limma microarray statistics
updated 8.0 years ago by 50k • written 8.0 years ago by • 0
8
votes
8
replies
6.7k
views
Voom transformation from counts and normalization to negative values
rnaseq voom limma tcga statistics
updated 5.6 years ago by ★ 7.9k • written 5.6 years ago by ▴ 60
3
votes
5
replies
1.3k
views
P adjusted values in Deseq2
DESeq2 Statistics
written 3.3 years ago by • 0
3
votes
0
replies
2.2k
views
Job: Postdoctoral Scientist, Statistical Bioinformatics and Proteomics, WEHI Australia
job proteomics Job statistics
4.5 years ago • updated 4.3 years ago Gordon Smyth 50k
3
votes
3
replies
1.4k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2 apeglm statistics
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
2
votes
2
replies
2.8k
views
How adjusted p-values are calculated in limma
limma r transcriptomics FDR statistics
updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 10
2
votes
1
reply
976
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
2
votes
3
replies
1.5k
views
RNAseq outlier is a critical sample
rnaseq outlier statistics batch effect
updated 7.9 years ago by 50k • written 7.9 years ago by • 0
2
votes
2
replies
7.6k
views
edgeR: How is FDR calculated for logFC? (False Discovery Rate)
edgeR bioconductor fdr statistics differential gene expression
7.4 years ago jol.espinoz ▴ 40
2
votes
4
replies
1.2k
views
Removing batch effect on edgeR when interactons are looked at
rnaseq edger statistics model matrix
updated 6.5 years ago by ★ 13k • written 6.6 years ago by ▴ 90
2
votes
0
replies
841
views
Job: Multiple open positions in biomedical statistics at Eurac Research, Italy
epidemiology statistics bioinformatics Job
3.6 years ago Johannes Rainer ★ 2.0k
1
vote
0
replies
751
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Job: Lecturer in Statistics - School of Mathematics and Statistics - University of St Andrews
computational teaching statistics research
21 months ago Andy Lynch ▴ 120
1
vote
0
replies
1.6k
views
Job: PhD Positions in Computational Cancer Research
computational biology image analysis cancer genomics statistics Job
7.4 years ago Bernd Fischer ▴ 550
1
vote
2
replies
2.7k
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the statistical test that DESeq2 use
deseq2 statistics
updated 7.2 years ago by ★ 7.9k • written 7.2 years ago by • 0
1
vote
1
reply
1.3k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 12 months ago by ★ 4.0k • written 12 months ago by • 0
1
vote
0
replies
1.2k
views
Job: Statistical Research Associate
biostatistics statistics sas git assay Job
6.0 years ago Fred Hutch (Recruiting) ▴ 40
1
vote
4
replies
1.2k
views
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
5.7 years ago Andrea Carenzo • 0
1
vote
2
replies
950
views
What to do with microarray probes that catch multiple genes?
affymetrix microarrays microarray probe statistics
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
1
vote
2
replies
926
views
Newbie to all of this
bioconductor statistics
5.5 years ago sportwoo • 0
1
vote
6
replies
2.7k
views
DESeq2 unbalanced sample size
deseq2 bioconductor bioinformatics statistics
updated 13 months ago by 41k • written 5.3 years ago by • 0
1
vote
0
replies
2.0k
views
Job: Postdoctoral Research Fellow in Bioinformatics - Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Mainz, Germany
bioinformatician job rnaseq statistics systemsbiology Job
9.0 years ago Federico Marini ▴ 150
1
vote
2
replies
2.0k
views
how to perform pre ranked GSEA in R?
r microarray statistics GSEA
updated 7.1 years ago by • 0 • written 9.1 years ago by ▴ 80
1
vote
0
replies
870
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Job: Post-Doctoral Research Fellow, Cancer Genomics
genomics seattle bioinformatics data science statistics Job
3.9 years ago Fred Hutch (Recruiting) ▴ 40
1
vote
2
replies
1.0k
views
Re-calculation of Padj (P adjusted value)
statistics Benjamini–Hochberg procedure deseq2
updated 3.5 years ago by 41k • written 3.5 years ago by ▴ 60
1
vote
0
replies
1.8k
views
News: Workshop Statistical Methods for Post Genomic Data in Munich, February 12-13, 2015
statistics workshop news News
9.6 years ago gagneur ▴ 10
1
vote
1
reply
334
views
Further analysis after limma regression output
statistics Epigenetics limma
updated 6 months ago by 65k • written 7 months ago by ▴ 10
1
vote
0
replies
615
views
Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
20 months ago arisarkar88 ▴ 40
1
vote
0
replies
732
views
Job: Research Fellow in Prostate Cancer Proteomics (Bioinformatics/Stats/Data Analysis) - University of St Andrews
Multiomics Proteomics Cancer Statistics Bioinformatics
21 months ago Andy Lynch ▴ 120
0
votes
2
replies
1.1k
views
comparing two GOstats result lists
gostats statistics
updated 5.9 years ago by 65k • written 5.9 years ago by ▴ 20
0
votes
0
replies
1.9k
views
Job: Postdoc and PhD student in Bioinformatics/Biostatistics
genomics NGS R genetics statistics
5.8 years ago • updated 3.4 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
899
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Job: Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
singlecellRNA-Seq pathview statistics R
3.1 years ago • updated 3.0 years ago Luo Weijun ★ 1.6k
0
votes
3
replies
1.4k
views
Reading large file (15GB) in R
R Rstudio Bioconducter statistics
updated 2.2 years ago by 21k • written 2.2 years ago by ▴ 10
0
votes
0
replies
1.5k
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Job: Come apply for our Epidemiologist, AncestryHealth role
genomics genetics design statistics scientist Job
8.8 years ago careers • 0
0
votes
2
replies
995
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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
2.5 years ago • updated 14 months ago Wolfgang Huber ★ 13k
0
votes
3
replies
912
views
batch effect in EPIC array data
statistics Epigenetics R
updated 14 months ago by ▴ 730 • written 14 months ago by ▴ 10
0
votes
0
replies
749
views
package for mismatch distribution?
genetics statistics
5.2 years ago myriam.croze07 • 0
0
votes
1
reply
960
views
Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS GWAS resampling resample statistics
5.2 years ago naglemi ▴ 10
0
votes
0
replies
1.3k
views
Job: Postdoc and PhD student in Bioinformatics/Biostatistics
NGS R statistics genomics big data Job
5.2 years ago • updated 4.4 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
636
views
Job: PhD position in Bioinformatics in Jena
Statistics ComputationalBiology Aging MachineLearning
15 months ago alena.vanboemmel • 0
0
votes
0
replies
984
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Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
4.7 years ago tatabox • 0
0
votes
0
replies
160
views
Job: Statistics Lectureships at St Andrews
JobPosting computational statistics
8 weeks ago Andy Lynch ▴ 120
0
votes
1
reply
752
views
Exclude interaction terms from the design
deseq2 statistics modelling
updated 4.5 years ago by 41k • written 4.5 years ago by • 0
0
votes
0
replies
2.0k
views
Job: Full position as Statistician at ETH Zurich in Personalized Medicine Consultancy/Data Analysis
statistics consultancy personalized medicine Job
9.5 years ago Daniel Stekhoven ▴ 10
0
votes
1
reply
760
views
How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression
4.4 years ago A • 0
0
votes
4
replies
2.8k
views
XCMS for targeted metabolomic/lipidomics/proteomics
xcms metabolomics lipidomics statistics
8.3 years ago Titan • 0
0
votes
0
replies
751
views
Job: Two Bioinformatics Fellowship Positions at US EPA
bioinformatics toxicology Job sequenicng statistics
3.7 years ago • updated 3.4 years ago whduke • 0
0
votes
1
reply
312
views
DEseq2 : Complex design with a mixture of male and female mice
statistics DESeq2
updated 4 months ago by 41k • written 4 months ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts by Michael Love 41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts by Michael Love 41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Comment: Estimating Cell Counts for EPIC V2 array data by normawiedman059 • 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
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A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
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