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PLAGE method fails in GSVA if an overlap between gene sets and genes in expressions is less than two
gsva plage differential expression gene set enrichment
3.4 years ago krassowski.michal ▴ 10
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Comment: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0 by Yang Shi • 0
Perfect answer! This questions troubled me for a long time. Thanks again and for your quick and detailed reply.
Comment: HTSeq Counts no longer available by swbarnes2 ★ 1.0k
STAR's output was intended to mimic HTseq-counts.
Answer: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0 by James W. MacDonald 59k
In the previous post I noted that `paCalls` doesn't exist for this array, and that is still true today. And there are no methods similar to…
Comment: DiffBind GreyListChIP error: Error: BiocParallel errors by Rory Stark ★ 4.4k
Could you let me know the versions? Output of `sessionInfo()`.
Comment: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o by Yang Shi • 0
okay sir, the new post is here (https://support.bioconductor.org/p/9144266/). Looking forward to your reply.
Votes
Answer: Variance explained (coefficient of determination) in edgeR
HTSeq Counts no longer available
Comment: Problem converting transcript to genomic coordinates with Annotation Hub
Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
C: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o
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Popular Question to Johannes Rainer ★ 1.9k
Popular Question to Gordon Smyth 45k
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Scholar to Hervé Pagès 15k
Commentator to James W. MacDonald 59k
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