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25
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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
votes
4
replies
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
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
1.4k
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
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
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
7.7k
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
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
2
votes
0
replies
846
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
761
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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
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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
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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
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
1
vote
2
replies
931
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 14 months ago by 41k • written 5.4 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
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2
replies
2.0k
views
how to perform pre ranked GSEA in R?
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updated 7.1 years ago by • 0 • written 9.1 years ago by ▴ 80
1
vote
0
replies
878
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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
1.1k
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
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
343
views
Further analysis after limma regression output
statistics Epigenetics limma
updated 7 months ago by 65k • written 7 months ago by ▴ 10
1
vote
0
replies
624
views
Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
20 months ago arisarkar88 ▴ 40
1
vote
0
replies
746
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
906
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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
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3
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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
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
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2
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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
0
votes
3
replies
925
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
756
views
package for mismatch distribution?
genetics statistics
5.3 years ago myriam.croze07 • 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
0
votes
0
replies
1.3k
views
Job: Postdoc and PhD student in Bioinformatics/Biostatistics
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5.2 years ago • updated 4.4 years ago Luo Weijun ★ 1.6k
0
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0
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647
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Job: PhD position in Bioinformatics in Jena
Statistics ComputationalBiology Aging MachineLearning
15 months ago alena.vanboemmel • 0
0
votes
0
replies
989
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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
170
views
Job: Statistics Lectureships at St Andrews
JobPosting computational statistics
8 weeks ago Andy Lynch ▴ 120
0
votes
1
reply
755
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
772
views
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
views
XCMS for targeted metabolomic/lipidomics/proteomics
xcms metabolomics lipidomics statistics
8.3 years ago Titan • 0
0
votes
0
replies
758
views
Job: Two Bioinformatics Fellowship Positions at US EPA
bioinformatics toxicology Job sequenicng statistics
3.7 years ago • updated 3.5 years ago whduke • 0
0
votes
1
reply
318
views
DEseq2 : Complex design with a mixture of male and female mice
statistics DESeq2
updated 4 months ago by 41k • written 5 months 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…
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C: when to apply quantile normalization with voom in limma/voom framework with RNA-
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A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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Answer: Log-cpm values from limma
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