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10
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14
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13k
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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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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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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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5
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P adjusted values in Deseq2
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written 3.3 years ago by • 0
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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4
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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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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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921
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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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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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1.5k
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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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Reading large file (15GB) in R
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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 5.6 years ago by 65k • written 5.7 years ago by • 0
0
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2
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683
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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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930
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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
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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 3.5 years ago by 41k • written 3.5 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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Further analysis after limma regression output
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updated 7 months ago by 65k • written 7 months ago by ▴ 10
0
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1
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769
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How to handle batch effect and interaction with experimental variables
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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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317
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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
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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
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980
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limma for gene expression analysis with big and unbalanced sample size
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50 results • Page 1 of 1
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Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
Please provide more information! In your first post you seem to report another error than in your 2nd post: `No gene can be mapped...` vers…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
I don't really have any additional suggestion here.
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Dear Michael, I tried all three ways (the orIginal, increasing the number of required samples,and subsetting (the countdata and metadata be…
Comment: DESeq2 - dispersion estimation when there is none by Michael Love 41k
The red line does assume that shape but the fact the black points show that pattern is discussed in the 2014 paper. > Some caution is warr…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
I don't really follow what you are saying. All you have to do is delete the NCBI.sqlite db and *re-run the script exactly as you did above.…
Votes
DESeq2: How to find out how well the model fits the data?
Comment: DESeq2 - dispersion estimation when there is none
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
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