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10
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14
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12k
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how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 2.7 years ago by ▴ 20 • written 7.8 years ago by ▴ 30
8
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8
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6.0k
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Voom transformation from counts and normalization to negative values
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updated 5.2 years ago by 7.8k • written 5.2 years ago by ▴ 50
25
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7
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Effect of lfcThreshold on p-value in DESeq2
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updated 8 weeks ago by ▴ 10 • written 6.1 years ago by ▴ 30
0
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6
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1.0k
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regression analysis for epic array methylation data using limma
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18 months ago Jitendra ▴ 10
1
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6
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DESeq2 unbalanced sample size
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updated 9 months ago by 41k • written 5.0 years ago by • 0
3
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P adjusted values in Deseq2
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written 2.9 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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8.2 years ago sunkid • 0
1
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4
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1.1k
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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
5.3 years ago Andrea Carenzo • 0
0
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4
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XCMS for targeted metabolomic/lipidomics/proteomics
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7.9 years ago Titan • 0
19
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Confidence intervals on edgeR logFC
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0
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10 multiple comparisons in DESeq2
deseq2 rnaseq statistics
updated 7.5 years ago by 41k • written 7.5 years ago by • 0
2
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4
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Removing batch effect on edgeR when interactons are looked at
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updated 6.2 years ago by 13k • written 6.2 years ago by ▴ 70
8
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3
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Differing topTable() results with Limma with and without specifying coefficient
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updated 7.6 years ago by 48k • written 7.6 years ago by • 0
0
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3
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Reading large file (15GB) in R
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updated 21 months ago by 21k • written 22 months ago by ▴ 10
2
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3
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RNAseq outlier is a critical sample
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updated 7.5 years ago by 48k • written 7.5 years ago by • 0
0
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3
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666
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batch effect in EPIC array data
statistics Epigenetics R
updated 9 months ago by ▴ 720 • written 9 months ago by ▴ 10
3
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3
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Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2 apeglm statistics
updated 4.5 years ago by 41k • written 4.5 years ago by • 0
2
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2
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How adjusted p-values are calculated in limma
limma r transcriptomics FDR statistics
updated 4.2 years ago by 48k • written 4.2 years ago by ▴ 10
1
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2
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how to perform pre ranked GSEA in R?
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updated 6.7 years ago by • 0 • written 8.8 years ago by ▴ 80
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Compute test-score statistical significance using control-scores from shuffled population
statistics hypotheses R
7.7 years ago Bade ▴ 310
2
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2
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7.1k
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edgeR: How is FDR calculated for logFC? (False Discovery Rate)
edgeR bioconductor fdr statistics differential gene expression
7.0 years ago jol.espinoz ▴ 40
1
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2
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the statistical test that DESeq2 use
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updated 6.8 years ago by 7.8k • written 6.8 years ago by • 0
0
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2
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956
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comparing two GOstats result lists
gostats statistics
updated 5.5 years ago by 64k • written 5.5 years ago by ▴ 20
1
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2
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824
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What to do with microarray probes that catch multiple genes?
affymetrix microarrays microarray probe statistics
updated 5.3 years ago by 64k • written 5.3 years ago by • 0
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Newbie to all of this
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5.1 years ago sportwoo • 0
1
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2
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864
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Re-calculation of Padj (P adjusted value)
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updated 3.2 years ago by 41k • written 3.2 years ago by ▴ 50
0
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Results analysis of differential gene expression using DESeq2 package
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updated 11 months ago by ★ 1.3k • written 11 months ago by • 0
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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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2.1 years ago • updated 10 months ago Wolfgang Huber 13k
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Further analysis after limma regression output
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Exclude interaction terms from the design
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FPKM t-test vs DEseq2
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limma for gene expression analysis with big and unbalanced sample size
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How to handle batch effect and interaction with experimental variables
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4.1 years ago A • 0
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DEseq2 : Complex design with a mixture of male and female mice
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Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
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Comment: GOslim missing GO term by amanda • 0
Thank you for the advice and many thanks! It is WGCNA analysis. I will try your method today and see if there are some consistencies.
Comment: GOslim missing GO term by James W. MacDonald 64k
Is this a WGCNA analysis (multiple co-expression clusters sounds like WGCNA)? If so, none of that is inferential or easily interpreted. It …
Comment: GOslim missing GO term by amanda • 0
For each group, I generated multiple co-expression clusters, and within each cluster, cluster PC1 was correlated with PC1 of multiple clini…
Comment: GOslim missing GO term by James W. MacDonald 64k
What do you mean by 'enriched with ... GO terms from their correlations with clinical traits'? Are you doing a GO hypergeometric or somethi…
Comment: GOslim missing GO term by amanda • 0
I have multiple groups to compare with, and each enriched with hundreds of GO terms from their correlations with clinical traits (top1 pval…
Votes
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: limma::voom vs edgeR::voomLmFit - when to use?
Answer: limma::voom vs edgeR::voomLmFit - when to use?
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