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10
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14
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13k
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how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 3.2 years ago by ▴ 20 • written 8.2 years ago by ▴ 30
8
votes
8
replies
6.8k
views
Voom transformation from counts and normalization to negative values
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updated 5.6 years ago by ★ 7.9k • written 5.6 years ago by ▴ 60
25
votes
7
replies
11k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 7 months ago by ▴ 10 • written 6.6 years ago by ▴ 30
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
1
vote
6
replies
2.8k
views
DESeq2 unbalanced sample size
deseq2 bioconductor bioinformatics statistics
updated 14 months ago by 41k • written 5.4 years ago by • 0
0
votes
5
replies
1.1k
views
Comparing sets of differentially expressed genes
deseq2 rnaseq statistics
8.6 years ago sunkid • 0
3
votes
5
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1.4k
views
P adjusted values in Deseq2
DESeq2 Statistics
written 3.3 years ago by • 0
0
votes
4
replies
2.8k
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XCMS for targeted metabolomic/lipidomics/proteomics
xcms metabolomics lipidomics statistics
8.3 years ago Titan • 0
19
votes
4
replies
8.1k
views
Confidence intervals on edgeR logFC
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updated 8.1 years ago by • 0 • written 9.6 years ago by ▴ 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
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
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
3
replies
953
views
batch effect in EPIC array data
statistics Epigenetics R
updated 14 months ago by ▴ 730 • written 14 months ago by ▴ 10
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
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
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
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
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
2
replies
2.1k
views
how to perform pre ranked GSEA in R?
r microarray statistics GSEA
updated 7.2 years ago by • 0 • written 9.2 years ago by ▴ 80
1
vote
2
replies
965
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
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
1
vote
2
replies
942
views
Newbie to all of this
bioconductor statistics
5.6 years ago sportwoo • 0
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
1
vote
2
replies
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
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
2
votes
2
replies
1.1k
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limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 5 days ago by • 0 • written 7.9 years ago by • 0
2
votes
2
replies
2.9k
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
2
replies
696
views
Results analysis of differential gene expression using DESeq2 package
RnaSeqSampleSize statistics DESeq2
updated 17 months ago by ★ 1.3k • written 17 months ago by • 0
0
votes
2
replies
1.0k
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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 15 months ago Wolfgang Huber ★ 13k
1
vote
1
reply
365
views
Further analysis after limma regression output
statistics Epigenetics limma
updated 7 months ago by 65k • written 7 months ago by ▴ 10
1
vote
1
reply
1.3k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
0
votes
1
reply
786
views
How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression
4.5 years ago A • 0
0
votes
1
reply
764
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
1
reply
327
views
DEseq2 : Complex design with a mixture of male and female mice
statistics DESeq2
updated 5 months ago by 41k • written 5 months ago by • 0
0
votes
1
reply
981
views
Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS GWAS resampling resample statistics
5.3 years ago naglemi ▴ 10
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 4.4 years ago Gordon Smyth 50k
1
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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
0
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Job: Two Bioinformatics Fellowship Positions at US EPA
bioinformatics toxicology Job sequenicng statistics
3.8 years ago • updated 3.5 years ago whduke • 0
2
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Job: Multiple open positions in biomedical statistics at Eurac Research, Italy
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Job: Bioinformatician at MiroBio, Oxford, UK
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multipollutant models
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5 months ago Jitendra ▴ 10
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Job: Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
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Job: Full position as Statistician at ETH Zurich in Personalized Medicine Consultancy/Data Analysis
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Job: Statistics Lectureships at St Andrews
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Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
21 months ago arisarkar88 ▴ 40
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Job: Research Fellow in Prostate Cancer Proteomics (Bioinformatics/Stats/Data Analysis) - University of St Andrews
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50 results • Page 1 of 1
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Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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