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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
8
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8
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6.7k
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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
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7
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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
0
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6
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1.3k
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regression analysis for epic array methylation data using limma
limma Epigenetics STATISTICS R
23 months ago Jitendra ▴ 10
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
0
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5
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1.1k
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Comparing sets of differentially expressed genes
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8.6 years ago sunkid • 0
3
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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
0
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4
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2.8k
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XCMS for targeted metabolomic/lipidomics/proteomics
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8.3 years ago Titan • 0
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
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
0
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4
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5.6k
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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
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1.2k
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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
936
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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
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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
2
votes
3
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1.5k
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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
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1.4k
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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
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1.5k
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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
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1.3k
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Compute test-score statistical significance using control-scores from shuffled population
statistics hypotheses R
8.1 years ago Bade ▴ 310
1
vote
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
vote
2
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956
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What to do with microarray probes that catch multiple genes?
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updated 5.7 years ago by 65k • written 5.7 years ago by • 0
0
votes
2
replies
687
views
Results analysis of differential gene expression using DESeq2 package
RnaSeqSampleSize statistics DESeq2
updated 16 months ago by ★ 1.3k • written 16 months ago by • 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
2
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2
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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
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
0
votes
2
replies
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
1
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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
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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
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
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
0
votes
1
reply
774
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How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression
4.5 years ago A • 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
0
votes
1
reply
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
1
reply
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
0
votes
1
reply
969
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Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
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5.2 years ago naglemi ▴ 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
3
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2.2k
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Job: Postdoctoral Scientist, Statistical Bioinformatics and Proteomics, WEHI Australia
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4.5 years ago • updated 4.3 years ago Gordon Smyth 50k
1
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Job: Post-Doctoral Research Fellow, Cancer Genomics
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3.9 years ago Fred Hutch (Recruiting) ▴ 40
0
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Job: Two Bioinformatics Fellowship Positions at US EPA
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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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0
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3.4 years ago • updated 3.1 years ago Luo Weijun ★ 1.6k
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3.3 years ago Laura • 0
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Job: Bioinformatician at MiroBio, Oxford, UK
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multipollutant models
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4 months ago Jitendra ▴ 10
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3.1 years ago • updated 3.0 years ago Luo Weijun ★ 1.6k
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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
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20 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: 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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