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Answer: A: how to use Normalized gene expression data in Deseq2?
9.1 years ago Ryan C. Thompson ★ 7.9k
2
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2.0k
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Answer: A: Limma Nuisance Variable in an Interaction Model
9.2 years ago Ryan C. Thompson ★ 7.9k
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1
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2.3k
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Comment: C: How to handle mix of samples from the same subject and from different subjects d
9.2 years ago Ryan C. Thompson ★ 7.9k
21
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1
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48k
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Answer: A: Batch correction in DESeq2
9.2 years ago Ryan C. Thompson ★ 7.9k
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2
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21k
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Comment: C: DESeq2 for ChIP-seq differential peaks
9.2 years ago Ryan C. Thompson ★ 7.9k
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1
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21k
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Comment: C: DESeq2 for ChIP-seq differential peaks
9.2 years ago Ryan C. Thompson ★ 7.9k
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2.3k
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Comment: C: How to handle mix of samples from the same subject and from different subjects d
9.2 years ago Ryan C. Thompson ★ 7.9k
2
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2
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2.3k
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Answer: A: How to handle mix of samples from the same subject and from different subjects d
9.2 years ago Ryan C. Thompson ★ 7.9k
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8.2k
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Comment: C: edger, trended or common dispersion
9.2 years ago Ryan C. Thompson ★ 7.9k
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3
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8.2k
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Comment: C: edger, trended or common dispersion
9.2 years ago Ryan C. Thompson ★ 7.9k
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1
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8.2k
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Answer: A: edger, trended or common dispersion
9.2 years ago Ryan C. Thompson ★ 7.9k
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3.6k
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Comment: C: Alpha diversity on Rlogtransformed data
9.2 years ago Ryan C. Thompson ★ 7.9k
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3
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1.5k
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Feature request for Rsubread::featureCounts: read length adjustment
updated 9.2 years ago by 52k • written 10.9 years ago by ★ 7.9k
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0
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1.0k
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Answer: A: deseq2: nice p.value but adjusted p value is NA
9.2 years ago Ryan C. Thompson ★ 7.9k
1
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0
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3.6k
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Comment: C: Finding the coordinates from a BCV plot in edgeR
9.2 years ago Ryan C. Thompson ★ 7.9k
1
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1
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3.6k
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Comment: C: Finding the coordinates from a BCV plot in edgeR
9.2 years ago Ryan C. Thompson ★ 7.9k
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12k
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Comment: C: Normalization of RNA-seq data: between samples and within samples
9.2 years ago Ryan C. Thompson ★ 7.9k
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0
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5.6k
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Comment: C: DESEQ2 with 3 biological replicates for control and 1 biological replicate for t
9.2 years ago Ryan C. Thompson ★ 7.9k
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2
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4.2k
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Comment: C: Low-count filtering with uneven sequencing depth between samples?
9.2 years ago Ryan C. Thompson ★ 7.9k
0
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0
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4.2k
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Comment: C: Low-count filtering with uneven sequencing depth between samples?
9.2 years ago Ryan C. Thompson ★ 7.9k
0
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1.2k
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Comment: C: Need assistance with complicated DESeq2 design
9.2 years ago Ryan C. Thompson ★ 7.9k
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1
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4.9k
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Comment: C: DESeq2 very slow with many samples
9.2 years ago Ryan C. Thompson ★ 7.9k
1
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1
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4.2k
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Comment: C: Low-count filtering with uneven sequencing depth between samples?
9.2 years ago Ryan C. Thompson ★ 7.9k
1
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1
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4.2k
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Comment: C: Low-count filtering with uneven sequencing depth between samples?
9.2 years ago Ryan C. Thompson ★ 7.9k
1
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1
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3.5k
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Comment: C: Interpretation of mroast gene set analysis in R and appropriate use of the funct
9.2 years ago Ryan C. Thompson ★ 7.9k
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1
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3.0k
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Comment: C: Joint Preprocessing of RNA-Seq and Microarray datasets
9.2 years ago Ryan C. Thompson ★ 7.9k
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1
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2.0k
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Comment: C: ANOVA in EdgeR
9.2 years ago Ryan C. Thompson ★ 7.9k
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1
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6.1k
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Answer: A: using DEseq2 for miRNA differential expression
9.2 years ago Ryan C. Thompson ★ 7.9k
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1
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6.7k
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Comment: C: Unable to use qvalue. Estimated pi0 is <=0
9.2 years ago Ryan C. Thompson ★ 7.9k
1
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0
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6.7k
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Comment: C: Unable to use qvalue. Estimated pi0 is <=0
9.2 years ago Ryan C. Thompson ★ 7.9k
0
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1
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1.2k
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Modeling a combination of synchronized and unsynchronized time points?
design matrix spline ns limma
updated 9.3 years ago by ★ 28k • written 9.3 years ago by ★ 7.9k
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1
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4.9k
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Answer: A: Can DESeq2 deal with zero-inflated data
9.3 years ago Ryan C. Thompson ★ 7.9k
6
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1
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36k
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Answer: A: FDR and padj in deseq and edger
9.3 years ago Ryan C. Thompson ★ 7.9k
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36k
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Comment: C: FDR and padj in deseq and edger
9.3 years ago Ryan C. Thompson ★ 7.9k
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1.0k
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Comment: C: The distribution function for zero-altered negative binomial density produces a
9.3 years ago Ryan C. Thompson ★ 7.9k
1
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1
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1.0k
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Answer: A: The distribution function for zero-altered negative binomial density produces a
9.3 years ago Ryan C. Thompson ★ 7.9k
6
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1
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11k
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Answer: A: Correct assumptions of using limma moderated t-test
9.7 years ago • updated 9.3 years ago Ryan C. Thompson ★ 7.9k
5
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0
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2.5k
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Answer: A: Appropriate explanation of the methodology behind arrayWeights function from lim
9.3 years ago Ryan C. Thompson ★ 7.9k
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0
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2.3k
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Answer: A: unexpected voom! / limma contrast inconsistency
updated 9.3 years ago by 52k • written 11.4 years ago by ★ 7.9k
1
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2
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3.0k
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Answer: A: normalized data by DESeq2 look suspicious
9.3 years ago Ryan C. Thompson ★ 7.9k
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0
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11k
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Comment: C: Estimating and removing batch effects from rna-seq dataset
9.3 years ago Ryan C. Thompson ★ 7.9k
1
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1
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2.0k
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Answer: A: Combination of duplicateCorrelation with arrayWeights to increase power for DE d
9.3 years ago Ryan C. Thompson ★ 7.9k
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2.0k
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Comment: C: Combination of duplicateCorrelation with arrayWeights to increase power for DE d
9.3 years ago Ryan C. Thompson ★ 7.9k
0
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1
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4.7k
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Comment: C: EdgeR - RNA-Seq time course analysis - Testing main and interaction effects and
9.3 years ago Ryan C. Thompson ★ 7.9k
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1
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3.8k
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Comment: C: Different results in edgeR using simple vs GLM
9.3 years ago Ryan C. Thompson ★ 7.9k
1
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0
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5.8k
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Comment: C: Using edgeR or DESeq2 to analyze allele-specific expression?
9.3 years ago Ryan C. Thompson ★ 7.9k
2
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1
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12k
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Answer: A: Normalization of RNA-seq data: between samples and within samples
9.4 years ago Ryan C. Thompson ★ 7.9k
1
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0
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12k
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Comment: C: Normalization of RNA-seq data: between samples and within samples
9.4 years ago Ryan C. Thompson ★ 7.9k
0
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1
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2.5k
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Comment: C: design matrix for cross-over + repeated measures in limma?
9.4 years ago Ryan C. Thompson ★ 7.9k
0
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1
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2.5k
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Answer: A: design matrix for cross-over + repeated measures in limma?
9.4 years ago Ryan C. Thompson ★ 7.9k
819 results • Page 9 of 17
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