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Comment: C: How to annotate DESeq2 object with gene size to get FPKMs
9.2 years ago Ryan C. Thompson ★ 7.9k
0
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1
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4.6k
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Comment: C: How to annotate DESeq2 object with gene size to get FPKMs
9.2 years ago Ryan C. Thompson ★ 7.9k
0
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1
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1.6k
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Comment: C: glmTreat() fails to shrink coefficients?
9.2 years ago Ryan C. Thompson ★ 7.9k
0
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2
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1.6k
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Answer: A: glmTreat() fails to shrink coefficients?
9.2 years ago Ryan C. Thompson ★ 7.9k
2
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0
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4.5k
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Comment: C: Limma camera function never gives any differentially expressed gene sets
9.2 years ago Ryan C. Thompson ★ 7.9k
0
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0
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2.3k
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Comment: C: trying to use ballgown with Sailfish/Salmon pipeline
9.2 years ago Ryan C. Thompson ★ 7.9k
1
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0
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4.0k
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Comment: C: EdgeR Multifactorial design with batch effect-trouble with defining contrasts
9.3 years ago Ryan C. Thompson ★ 7.9k
2
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2
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4.0k
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Answer: A: EdgeR Multifactorial design with batch effect-trouble with defining contrasts
9.3 years ago Ryan C. Thompson ★ 7.9k
3
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0
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4.1k
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Comment: C: Log fold change on Limma
9.3 years ago Ryan C. Thompson ★ 7.9k
0
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1
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1.7k
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Comment: C: Multiple Testing Correction
9.3 years ago Ryan C. Thompson ★ 7.9k
2
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1
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4.1k
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Comment: C: Log fold change on Limma
9.3 years ago Ryan C. Thompson ★ 7.9k
2
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1
reply
4.1k
views
Answer: A: Log fold change on Limma
9.3 years ago Ryan C. Thompson ★ 7.9k
0
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0
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6.8k
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Comment: C: Rsubread::featureCounts extremely slow on some annotations
9.3 years ago Ryan C. Thompson ★ 7.9k
0
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1
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2.0k
views
Comment: C: edgeR (3.10.2) contrast question for experimental factors combined as a group
9.3 years ago Ryan C. Thompson ★ 7.9k
3
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1
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2.0k
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Answer: A: edgeR (3.10.2) contrast question for experimental factors combined as a group
9.3 years ago Ryan C. Thompson ★ 7.9k
0
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0
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7.9k
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Comment: C: Multiple alignments (multi-mapped reads) and DESeq/edgeR pipeline
9.3 years ago Ryan C. Thompson ★ 7.9k
0
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2
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2.5k
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Answer: A: Design and independent filtering of patient RNA-seq data
9.3 years ago Ryan C. Thompson ★ 7.9k
18
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12
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4.0k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 9.3 years ago by 42k • written 9.3 years ago by ★ 7.9k
0
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1
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7.9k
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Comment: C: Multiple alignments (multi-mapped reads) and DESeq/edgeR pipeline
9.3 years ago Ryan C. Thompson ★ 7.9k
0
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1
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1.9k
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Comment: C: NaN results on some pathways in CAMERA
9.3 years ago Ryan C. Thompson ★ 7.9k
8
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4
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1.9k
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NaN results on some pathways in CAMERA
camera edger pathway analysis
updated 9.3 years ago by 51k • written 9.3 years ago by ★ 7.9k
1
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1
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7.9k
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Comment: C: Multiple alignments (multi-mapped reads) and DESeq/edgeR pipeline
9.3 years ago Ryan C. Thompson ★ 7.9k
0
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0
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1.9k
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Comment: C: NaN results on some pathways in CAMERA
9.3 years ago Ryan C. Thompson ★ 7.9k
1
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1
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6.5k
views
Comment: C: DESeq2 variance transformation error and plot dispersion Estimate
9.3 years ago Ryan C. Thompson ★ 7.9k
1
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0
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6.1k
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Comment: C: Multiple Comparisons EdgeR
9.3 years ago Ryan C. Thompson ★ 7.9k
3
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2
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6.1k
views
Answer: A: Multiple Comparisons EdgeR
9.3 years ago Ryan C. Thompson ★ 7.9k
12
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10
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6.9k
views
edgeR glmLRT with test="F"?
edger dge differential expression
updated 9.3 years ago by ★ 28k • written 9.3 years ago by ★ 7.9k
1
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1
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5.0k
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Comment: C: Bootstrap confidence intervals on RNA-seq expression from Kallisto
9.3 years ago Ryan C. Thompson ★ 7.9k
1
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0
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1.4k
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Answer: A: EdgeR--multi-factorial nested design
9.3 years ago Ryan C. Thompson ★ 7.9k
0
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0
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4.4k
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Comment: C: edgeR design matrix
9.3 years ago Ryan C. Thompson ★ 7.9k
0
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0
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1.7k
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Comment: C: How many 'expressed genes' do I have in my dataset?
9.4 years ago Ryan C. Thompson ★ 7.9k
0
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0
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1.1k
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Answer: A: On DESeq, Extracting specific comparisons from multifactor designs
9.4 years ago Ryan C. Thompson ★ 7.9k
0
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0
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1.1k
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Comment: C: On DESeq, Extracting specific comparisons from multifactor designs
9.4 years ago Ryan C. Thompson ★ 7.9k
2
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1
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1.1k
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Are the endpoints included in intervals for SAF format?
rsubread featurecounts saf
9.4 years ago Ryan C. Thompson ★ 7.9k
1
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0
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3.6k
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Answer: A: Different clustering results of DESeq2 counts and rlog
9.4 years ago Ryan C. Thompson ★ 7.9k
3
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2
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2.8k
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Answer: A: Ribosome profiling analysis in DEseq2/limma
9.4 years ago Ryan C. Thompson ★ 7.9k
0
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0
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6.8k
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Comment: C: Rsubread::featureCounts extremely slow on some annotations
9.4 years ago Ryan C. Thompson ★ 7.9k
0
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0
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6.8k
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Comment: C: Rsubread::featureCounts extremely slow on some annotations
9.4 years ago Ryan C. Thompson ★ 7.9k
0
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0
replies
6.8k
views
Comment: C: Rsubread::featureCounts extremely slow on some annotations
9.4 years ago Ryan C. Thompson ★ 7.9k
0
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0
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6.8k
views
Comment: C: Rsubread::featureCounts extremely slow on some annotations
9.4 years ago Ryan C. Thompson ★ 7.9k
0
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0
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6.8k
views
Comment: C: Rsubread::featureCounts extremely slow on some annotations
9.4 years ago Ryan C. Thompson ★ 7.9k
0
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0
replies
6.8k
views
Comment: C: Rsubread::featureCounts extremely slow on some annotations
9.4 years ago Ryan C. Thompson ★ 7.9k
4
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1
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7.2k
views
Answer: A: Low percentage of assigned fragments with FeatureCounts
9.5 years ago Ryan C. Thompson ★ 7.9k
1
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0
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2.8k
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Comment: C: Gene expression between two copies of same gene:use counts or RPKM or FPKM?
9.5 years ago Ryan C. Thompson ★ 7.9k
1
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1
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2.2k
views
Comment: C: Add up RLEs that are in lists?
9.5 years ago Ryan C. Thompson ★ 7.9k
0
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1
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2.2k
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Answer: A: Add up RLEs that are in lists?
9.5 years ago Ryan C. Thompson ★ 7.9k
0
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0
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1.7k
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Answer: A: Nested Comparison using DESeq2
9.5 years ago Ryan C. Thompson ★ 7.9k
2
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1
reply
12k
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Comment: C: Removing continuous covariate effects in limma analysis
9.5 years ago Ryan C. Thompson ★ 7.9k
0
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0
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1.8k
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Comment: C: Correlation of a Linear Variable
9.5 years ago Ryan C. Thompson ★ 7.9k
1
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0
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6.4k
views
Comment: C: Limma for RNA-seq data
9.5 years ago Ryan C. Thompson ★ 7.9k
819 results • Page 11 of 17
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