Showing : statistics • reset
10
votes
14
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13k
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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
25
votes
7
replies
11k
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
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8.1k
views
Confidence intervals on edgeR logFC
edgeR statistics confidence interval
updated 8.1 years ago by • 0 • written 9.6 years ago by ▴ 40
2
votes
2
replies
7.7k
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
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
0
votes
4
replies
5.6k
views
10 multiple comparisons in DESeq2
deseq2 rnaseq statistics
updated 7.9 years ago by 41k • written 7.9 years ago by • 0
8
votes
3
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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
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
0
votes
4
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2.8k
views
XCMS for targeted metabolomic/lipidomics/proteomics
xcms metabolomics lipidomics statistics
8.3 years ago Titan • 0
1
vote
6
replies
2.7k
views
DESeq2 unbalanced sample size
deseq2 bioconductor bioinformatics statistics
updated 14 months ago by 41k • written 5.4 years ago by • 0
1
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2
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2.7k
views
the statistical test that DESeq2 use
deseq2 statistics
updated 7.2 years ago by ★ 7.9k • written 7.2 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
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
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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
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
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
1.9k
views
News: Workshop on Statistical Challenges in Single-Cell Biology, April 30 to May 5, 2017, at Villa Monte Verita, Ascona
workshop statistics single-cell News
7.7 years ago Wolfgang Huber ★ 13k
0
votes
0
replies
1.8k
views
Job: Bioinformatics Programmer (Statistician) at University of California at San Francisco
R bioinformatician job Perl Python statistics Job
8.0 years ago • updated 7.7 years ago clif.duhn • 0
1
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0
replies
1.8k
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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
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
0
votes
0
replies
1.6k
views
Job: Computational Biologist (Genome Statistical Analyst) position in CRUK Manchester Institute, UK
job bioinformatics ngs genomics statistics Job
8.2 years ago Hui Sun Leong ▴ 10
0
votes
0
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1.5k
views
Job: Research Scientist in Biostatistics/Bioinformatics
statistics genetics genomics R Job
7.2 years ago • updated 7.0 years ago Luo Weijun ★ 1.6k
2
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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
0
votes
0
replies
1.5k
views
Job: Come apply for our Epidemiologist, AncestryHealth role
genomics genetics design statistics scientist Job
8.8 years ago careers • 0
0
votes
3
replies
1.5k
views
Reading large file (15GB) in R
R Rstudio Bioconducter statistics
updated 2.2 years ago by 21k • written 2.3 years ago by ▴ 10
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
3
votes
5
replies
1.4k
views
P adjusted values in Deseq2
DESeq2 Statistics
written 3.3 years ago by • 0
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
2
replies
1.3k
views
Compute test-score statistical significance using control-scores from shuffled population
statistics hypotheses R
8.1 years ago Bade ▴ 310
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
0
votes
6
replies
1.3k
views
regression analysis for epic array methylation data using limma
limma Epigenetics STATISTICS R
23 months ago Jitendra ▴ 10
0
votes
0
replies
1.3k
views
Job: Bioinformaticist, Research Programmer
R genomics statistics Job
7.2 years ago radel • 0
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
0
votes
0
replies
1.2k
views
Job: Postdoc in Biostatistics/Bioinformatics at UNC Charlotte, NC, USA
genetics/genomics omics data statistics development R Job
7.7 years ago • updated 7.6 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
1.2k
views
Job: Seeking computational biologists with expertise in RNA-Seq and/or statistics at Immuneering Corporation, Cambridge MA and New York NY
rna-seq CNS Neurodegeneration statistics computational biology Job
7.5 years ago mmartin ▴ 20
2
votes
4
replies
1.2k
views
Removing batch effect on edgeR when interactons are looked at
rnaseq edger statistics model matrix
updated 6.6 years ago by ★ 13k • written 6.6 years ago by ▴ 90
0
votes
0
replies
1.2k
views
DSS DMLTest Prior Estimate of theta dispersion
DSS dmltest bayesian statistics methylation
6.0 years ago floriandeckert ▴ 30
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
0
votes
0
replies
1.2k
views
Assigning stats to differential peak locations relative to TSS
chipseeker chipseq statistics
6.6 years ago rbronste ▴ 60
0
votes
0
replies
1.2k
views
Two questions about pathifier package
pathways statistics microarray
6.3 years ago arronar • 0
0
votes
5
replies
1.1k
views
Comparing sets of differentially expressed genes
deseq2 rnaseq statistics
8.6 years ago • updated 8.5 years ago sunkid • 0
0
votes
0
replies
1.1k
views
News: SCANGEN: Single-cell cancer genomics workshop at ISMB 2018
single cell cancer genomics statistics News
6.1 years ago kieranrcampbell ▴ 50
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
1.1k
views
Job: Proteomics Bioinformatician
JobPosting Proteomics Statistics Job
3.3 years ago Laura • 0
1
vote
2
replies
1.1k
views
Re-calculation of Padj (P adjusted value)
statistics Benjamini–Hochberg procedure deseq2
updated 3.6 years ago by 41k • written 3.6 years ago by ▴ 60
0
votes
2
replies
1.0k
views
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 15 months ago Wolfgang Huber ★ 13k
0
votes
0
replies
989
views
Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
4.7 years ago tatabox • 0
2
votes
1
reply
981
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
0
votes
1
reply
965
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
1
vote
2
replies
954
views
What to do with microarray probes that catch multiple genes?
affymetrix microarrays microarray probe statistics
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
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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