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Answer: Answer: Limma for paired and unpaired samples. Strange number of DEGs in unpaired sample
3.3 years ago by Gordon Smyth ★ 8.3k
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3
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5.3k
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Answer: Answer: How to regress out age and sex using limma removeBatchEffect
3.3 years ago by Gordon Smyth ★ 8.3k
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2.4k
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Answer: Answer: How to choose threshold for filtering low counts before Voom transformation?
3.3 years ago by Gordon Smyth ★ 8.3k
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1.0k
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Answer: Answer: Limma false positives
3.4 years ago by Gordon Smyth ★ 8.3k
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1.3k
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Answer: Answer: Two rounds of batch effect removal
3.4 years ago by Gordon Smyth ★ 8.3k
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1.2k
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Answer: Answer: What should I expect to see for chromosome Y gene expression in a male mouse sam
3.4 years ago by Gordon Smyth ★ 8.3k
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5.6k
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Comment: Comment: Exclude pseudogenes and lncRNA's from DE-analysis?
3.4 years ago by Gordon Smyth ★ 8.3k
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4.0k
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Answer: Answer: Filtering lowly expressed genes
3.4 years ago by Gordon Smyth ★ 8.3k
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1.8k
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Comment: Comment: Advice on designing an EdgeR object in complex experimental setup ?
3.4 years ago by Gordon Smyth ★ 8.3k
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1.4k
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Comment: Comment: RNA-seq analysis without replicate
3.4 years ago by Gordon Smyth ★ 8.3k
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1.7k
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Answer: Answer: How to narrow down the Differential analysis gene list?
3.4 years ago by Gordon Smyth ★ 8.3k
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1.6k
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Answer: Answer: P.adjusted values
3.4 years ago by Gordon Smyth ★ 8.3k
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2.3k
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Comment: Comment: Flatten a GTF
3.4 years ago by Gordon Smyth ★ 8.3k
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1.1k
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Comment: Comment: edgeR
3.4 years ago by Gordon Smyth ★ 8.3k
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1.4k
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Answer: Answer: RNA-seq analysis without replicate
3.4 years ago by Gordon Smyth ★ 8.3k
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1
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2.3k
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Answer: Answer: Flatten a GTF
3.4 years ago by Gordon Smyth ★ 8.3k
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2.3k
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Comment: Comment: Unrealistic limma p-value
3.5 years ago by Gordon Smyth ★ 8.3k
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1
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2.3k
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Comment: Comment: Unrealistic limma p-value
3.5 years ago by Gordon Smyth ★ 8.3k
6
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1
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2.3k
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Answer: Answer: Unrealistic limma p-value
3.5 years ago by Gordon Smyth ★ 8.3k
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1.4k
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Answer: Answer: GCRMA normalization from data frame
3.5 years ago by Gordon Smyth ★ 8.3k
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868
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Answer: Answer: How to perform differential gene expression analysis from RMA and GCRMA normaliz
3.5 years ago by Gordon Smyth ★ 8.3k
5
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1.1k
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Answer: Answer: Formula for Differential Expression Analysis of 2 conditions and 2 cell types
3.5 years ago by Gordon Smyth ★ 8.3k
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1.9k
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Comment: Comment: EdgeR, a few DEGs found between group comparison, Can I go to further downstream
3.5 years ago by Gordon Smyth ★ 8.3k
2
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1
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1.9k
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Answer: Answer: EdgeR, a few DEGs found between group comparison, Can I go to further downstream
3.5 years ago by Gordon Smyth ★ 8.3k
0
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2
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1.9k
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Comment: Comment: EdgeR, a few DEGs found between group comparison, Can I go to further downstream
3.5 years ago by Gordon Smyth ★ 8.3k
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0
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2.1k
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Comment: Comment: Normalize ChIP-seq samples with different signal-to-noise ratio
3.5 years ago by Gordon Smyth ★ 8.3k
2
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1.7k
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Answer: Answer: My PCA plot looks good but i don't have differentially expressed genes
3.5 years ago by Gordon Smyth ★ 8.3k
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0
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3.5k
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Answer: Answer: Edge R, Error in data.frame(..., check.names = FALSE) : arguments imply diffe
3.5 years ago by Gordon Smyth ★ 8.3k
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0
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1.9k
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Answer: Answer: Use of detection scores in bead array
3.5 years ago by Gordon Smyth ★ 8.3k
1
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1
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1.7k
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Comment: Comment: Processing Illumina HumanHT-12 V4.0 data without detection p-values
3.5 years ago by Gordon Smyth ★ 8.3k
5
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1
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1.7k
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Answer: Answer: Processing Illumina HumanHT-12 V4.0 data without detection p-values
3.5 years ago by Gordon Smyth ★ 8.3k
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0
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1.0k
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Answer: Answer: NCBI H.Sapiens OrgDb missing many EntrezIDs
3.5 years ago by Gordon Smyth ★ 8.3k
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0
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2.1k
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Comment: Comment: In RNA-Seq data modeling process, glmfit function in R used raw RNA-Seq count da
3.6 years ago by Gordon Smyth ★ 8.3k
0
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1
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2.1k
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Comment: Comment: In RNA-Seq data modeling process, glmfit function in R used raw RNA-Seq count da
3.6 years ago by Gordon Smyth ★ 8.3k
1
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2
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2.1k
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Answer: Answer: In RNA-Seq data modeling process, glmfit function in R used raw RNA-Seq count da
3.6 years ago by Gordon Smyth ★ 8.3k
0
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0
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704
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Answer: Answer: Question on DE analysis for developing cell populations
3.6 years ago by Gordon Smyth ★ 8.3k
1
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0
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3.2k
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Answer: Answer: heatmaps for limma-voom DE genes
3.6 years ago by Gordon Smyth ★ 8.3k
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0
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2.0k
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Comment: Comment: Whether the probe intensity of microarray can be used to calculate TPM like the
3.6 years ago by Gordon Smyth ★ 8.3k
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1
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2.9k
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Comment: Comment: Is there any way to create MA plot with edgeR output?
3.6 years ago by Gordon Smyth ★ 8.3k
2
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1
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2.9k
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Answer: Answer: Is there any way to create MA plot with edgeR output?
3.6 years ago by Gordon Smyth ★ 8.3k
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0
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7.5k
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Comment: Comment: Limma Differential Analysis on Proteomics data
3.6 years ago by Gordon Smyth ★ 8.3k
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0
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7.5k
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Comment: Comment: Limma Differential Analysis on Proteomics data
3.6 years ago by Gordon Smyth ★ 8.3k
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0
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7.5k
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Comment: Comment: Limma Differential Analysis on Proteomics data
3.6 years ago by Gordon Smyth ★ 8.3k
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2
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7.5k
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Comment: Comment: Limma Differential Analysis on Proteomics data
3.6 years ago by Gordon Smyth ★ 8.3k
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0
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7.5k
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Comment: Comment: Limma Differential Analysis on Proteomics data
3.6 years ago by Gordon Smyth ★ 8.3k
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0
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1.3k
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Answer: Answer: Error in DEqMS proteomics analysis
3.6 years ago by Gordon Smyth ★ 8.3k
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1
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7.5k
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Answer: Answer: Limma Differential Analysis on Proteomics data
3.6 years ago by Gordon Smyth ★ 8.3k
2
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0
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2.8k
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Answer: Answer: Are the upregulated genes in one comparison the downregulated genes in the inver
3.6 years ago by Gordon Smyth ★ 8.3k
1
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0
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1.7k
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Comment: Comment: I have problem with pairwise comparison in estimate dispersion functions in edge
3.6 years ago by Gordon Smyth ★ 8.3k
2
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0
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1.4k
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Comment: Comment: Is it normal for most data to be lost when filtering data?
3.6 years ago by Gordon Smyth ★ 8.3k
577 results • Page 6 of 12
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