Showing : TCGA • reset
1
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2
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5.0k
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Differential Analysis for gene expression from TCGA (Level 3)
limma microarray tcga
updated 10.6 years ago by ★ 13k • written 10.6 years ago by • 0
0
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0
replies
2.7k
views
TCGA RSEM normalized RNAseqV2 counts
normalization cancer tcga
10.6 years ago ezz • 0
13
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20
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15k
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Can I feed TCGA normalized count data to EdgeR for differential gene expression analysis
EdgeR TCGA normalized count
updated 10.6 years ago by ▴ 130 • written 10.6 years ago by ▴ 20
5
votes
6
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7.7k
views
proper transformation for differential expression in normalized log expression data
tcga rnaseq deseq2 vsn edger
updated 10.8 years ago by 53k • written 10.8 years ago by • 0
9
votes
9
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6.1k
views
Voom on TCGA data shifts count distributions towards negative values
voom TCGA RNAseq
10.9 years ago paola.ostano ▴ 10
105 results • Page 3 of 3
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Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Answer: Streamlining the computing time for MiloDE p-value correction in large dataset? by Kevin Blighe ★ 4.0k
Hi Joseph, I agree with ATpoint's suggestion that pseudobulk aggregation (e.g., via aggregateData in scran or similar) would likely be far…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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