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25
votes
7
replies
11k
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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
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4
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8.1k
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Confidence intervals on edgeR logFC
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updated 8.1 years ago by • 0 • written 9.6 years ago by ▴ 40
10
votes
14
replies
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
8
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3
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3.2k
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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
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8
replies
6.7k
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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
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1.4k
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P adjusted values in Deseq2
DESeq2 Statistics
written 3.3 years ago by • 0
3
votes
0
replies
2.2k
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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
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Using alternative LFC shrinkage methods for computing p-values in DESeq2
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updated 4.9 years ago by 41k • written 4.9 years ago by • 0
2
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2
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2.8k
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How adjusted p-values are calculated in limma
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updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 10
2
votes
1
reply
983
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
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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
2
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2
replies
7.7k
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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
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1.2k
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Removing batch effect on edgeR when interactons are looked at
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updated 6.6 years ago by ★ 13k • written 6.6 years ago by ▴ 90
2
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0
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849
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Job: Multiple open positions in biomedical statistics at Eurac Research, Italy
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3.6 years ago Johannes Rainer ★ 2.0k
1
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764
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Job: Lecturer in Statistics - School of Mathematics and Statistics - University of St Andrews
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21 months ago Andy Lynch ▴ 120
1
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1.6k
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Job: PhD Positions in Computational Cancer Research
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7.4 years ago Bernd Fischer ▴ 550
1
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2
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2.7k
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the statistical test that DESeq2 use
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updated 7.2 years ago by ★ 7.9k • written 7.2 years ago by • 0
1
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1
reply
1.3k
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FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 12 months ago by ★ 4.0k • written 12 months ago by • 0
1
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0
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1.2k
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Job: Statistical Research Associate
biostatistics statistics sas git assay Job
6.0 years ago Fred Hutch (Recruiting) ▴ 40
1
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4
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1.2k
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Do the gene set statistics of the ROAST paper correspond to those implemented in the .roastEffects R function?
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5.7 years ago Andrea Carenzo • 0
1
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2
replies
956
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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
1
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2
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931
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Newbie to all of this
bioconductor statistics
5.5 years ago sportwoo • 0
1
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6
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2.7k
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DESeq2 unbalanced sample size
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updated 14 months ago by 41k • written 5.4 years ago by • 0
1
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0
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2.0k
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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
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2
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2.1k
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how to perform pre ranked GSEA in R?
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updated 7.1 years ago by • 0 • written 9.2 years ago by ▴ 80
1
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0
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880
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Job: Post-Doctoral Research Fellow, Cancer Genomics
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3.9 years ago Fred Hutch (Recruiting) ▴ 40
1
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2
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1.1k
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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
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
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1
reply
347
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Further analysis after limma regression output
statistics Epigenetics limma
updated 7 months ago by 65k • written 7 months ago by ▴ 10
1
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0
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629
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Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
20 months ago arisarkar88 ▴ 40
1
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0
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749
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Job: Research Fellow in Prostate Cancer Proteomics (Bioinformatics/Stats/Data Analysis) - University of St Andrews
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21 months ago Andy Lynch ▴ 120
0
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2
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1.1k
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comparing two GOstats result lists
gostats statistics
updated 5.9 years ago by 65k • written 5.9 years ago by ▴ 20
0
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Job: Postdoc and PhD student in Bioinformatics/Biostatistics
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5.8 years ago • updated 3.4 years ago Luo Weijun ★ 1.6k
0
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909
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3.1 years ago • updated 3.0 years ago Luo Weijun ★ 1.6k
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3
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Reading large file (15GB) in R
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updated 2.2 years ago by 21k • written 2.3 years ago by ▴ 10
0
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0
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1.5k
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Job: Come apply for our Epidemiologist, AncestryHealth role
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8.8 years ago careers • 0
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2
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News: Ascona Workshop “Biological systems: from first principles to data-​driven modelling and back” 27. 3. - 1. 4. 2022
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2.5 years ago • updated 15 months ago Wolfgang Huber ★ 13k
0
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3
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936
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batch effect in EPIC array data
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updated 14 months ago by ▴ 730 • written 14 months ago by ▴ 10
0
votes
0
replies
757
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package for mismatch distribution?
genetics statistics
5.3 years ago myriam.croze07 • 0
0
votes
1
reply
969
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
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0
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1.3k
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5.2 years ago • updated 4.4 years ago Luo Weijun ★ 1.6k
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15 months ago alena.vanboemmel • 0
0
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993
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Proteomics data analysis with DEP no replicates
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4.7 years ago tatabox • 0
0
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0
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174
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Job: Statistics Lectureships at St Andrews
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9 weeks ago Andy Lynch ▴ 120
0
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1
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757
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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
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9.5 years ago Daniel Stekhoven ▴ 10
0
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1
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773
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How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression
4.5 years ago A • 0
0
votes
4
replies
2.8k
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XCMS for targeted metabolomic/lipidomics/proteomics
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8.3 years ago Titan • 0
0
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0
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761
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3.8 years ago • updated 3.5 years ago whduke • 0
0
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1
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318
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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
50 results • Page 1 of 1
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Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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