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10
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14
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how DESeq calculates p-value ?
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updated 3.1 years ago by ▴ 20 • written 8.2 years ago by ▴ 30
8
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updated 5.6 years ago by ★ 7.9k • written 5.6 years ago by ▴ 60
25
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Effect of lfcThreshold on p-value in DESeq2
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updated 6 months ago by ▴ 10 • written 6.5 years ago by ▴ 30
0
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regression analysis for epic array methylation data using limma
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23 months ago Jitendra ▴ 10
1
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6
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DESeq2 unbalanced sample size
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updated 14 months ago by 41k • written 5.3 years ago by • 0
0
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Comparing sets of differentially expressed genes
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8.5 years ago sunkid • 0
3
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P adjusted values in Deseq2
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written 3.3 years ago by • 0
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4
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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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Confidence intervals on edgeR logFC
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1
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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
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4
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10 multiple comparisons in DESeq2
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updated 7.9 years ago by 41k • written 7.9 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 6.6 years ago by ★ 13k • written 6.6 years ago by ▴ 90
0
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3
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922
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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
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
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updated 8.0 years ago by 50k • written 8.0 years ago by • 0
2
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3
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RNAseq outlier is a critical sample
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updated 7.9 years ago by 50k • written 7.9 years ago by • 0
3
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3
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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
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3
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updated 2.2 years ago by 21k • written 2.3 years ago by ▴ 10
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Compute test-score statistical significance using control-scores from shuffled population
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8.1 years ago Bade ▴ 310
1
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2
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how to perform pre ranked GSEA in R?
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updated 7.1 years ago by • 0 • written 9.1 years ago by ▴ 80
1
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2
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954
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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
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2
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684
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Results analysis of differential gene expression using DESeq2 package
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updated 16 months ago by ★ 1.3k • written 16 months ago by • 0
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2
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1000
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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)
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7.4 years ago jol.espinoz ▴ 40
1
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2
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Newbie to all of this
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5.5 years ago sportwoo • 0
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2
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comparing two GOstats result lists
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updated 5.9 years ago by 65k • written 5.9 years ago by ▴ 20
1
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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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Re-calculation of Padj (P adjusted value)
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updated 3.6 years ago by 41k • written 3.6 years ago by ▴ 60
2
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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
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341
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Further analysis after limma regression output
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updated 7 months ago by 65k • written 7 months ago by ▴ 10
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770
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How to handle batch effect and interaction with experimental variables
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4.4 years ago A • 0
1
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1
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FPKM t-test vs DEseq2
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updated 12 months ago by ★ 4.0k • written 12 months ago by • 0
0
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755
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Exclude interaction terms from the design
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updated 4.5 years ago by 41k • written 4.5 years ago by • 0
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318
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DEseq2 : Complex design with a mixture of male and female mice
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updated 4 months ago by 41k • written 5 months ago by • 0
0
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Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
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981
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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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