Moderator: Kevin Blighe
Kevin Blighe ♦ 59k
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- Last seen:
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- Joined:
- 2 years, 9 months ago
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- k****@clinicalbioinformatics.co.uk
I am from the Republic of Ireland and have worked with dozens of universities, private companies, healthcare providers, and research institutes across the World, effectively functioning as a self-funded, independent research lab.
I contribute to the European Commission as an Expert Monitor, and also Moderate on the Biostars and Bioconductor support communities.
Developer / Maintainer of Bioconductor packages:
- EnhancedVolcano
- RegParallel
- PCAtools
- scDataviz (submitted)
Other packages:
LinkedIn: https://www.linkedin.com/in/clinicalbioinformatics/
Posts by Kevin Blighe
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... For clusterProfiler, you just need Entrez IDs, and you have those via the code that I shared in the previous answer. ...
written 2 hours ago by
Kevin Blighe ♦ 59k
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... Are you implying that you do not see this output when you run this command [?]:
keytypes(org.EcK12.eg.db)
[1] "ACCNUM" "ALIAS" "ENTREZID" "ENZYME" "EVIDENCE"
[6] "EVIDENCEALL" "GENENAME" "GO" "GOALL" "ONTOLOGY"
[11] "ONTOLOGYALL" "PATH" ...
written 3 hours ago by
Kevin Blighe ♦ 59k
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... I would not use raw read counts for PCA ...
written 3 hours ago by
Kevin Blighe ♦ 59k
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... I encountered this error only once in the past. It is as stated: every gene in your data has at least one zero value, and this creates an issue for the size-factor calculation.
Solutions:
1. add a pseudo-count value of '1' to your data
2. use: `estimateSizeFactors(dds_PvsN, type = 'iterate')`
K ...
written 12 hours ago by
Kevin Blighe ♦ 59k
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... I and colleague Asaf gave an answer here: https://www.biostars.org/p/440175/#440368
> I see - thanks. You can calculate TPM from the BRCA_mat object;
> however, you will still require the gene lengths. The TPM calculation
> is elaborated ere:
> https://www.rna-seqblog.com/rpkm-fpkm-and ...
written 14 hours ago by
Kevin Blighe ♦ 59k
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... Hey Rohit, thanks for coming back to explain - means a lot. Unfortunately, I don't have much to add due to the fact that the last time that I used DEXSeq was in 2016. I imagine that it is very difficult (for any program) to account for every possible splice-configuration, though. For what it's worth ...
written 14 hours ago by
Kevin Blighe ♦ 59k
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... I see - thanks. You can calculate TPM from the *BRCA_mat* object; however, you will still require the gene lengths. The TPM calculation is elaborated ere: https://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained.
DESeq2 does not produce TPM data. However, you could easily use DESeq2 to produ ...
written 14 hours ago by
Kevin Blighe ♦ 59k
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... Hey again, you have KEGG IDs from my previous answer (see 'PATH' column): https://www.biostars.org/p/439972/#439994
Kevin ...
written 15 hours ago by
Kevin Blighe ♦ 59k
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... Use `blind=TRUE` for QC (box-and-whiskers, PCA, unsupervised clustering, etc), but `blind=FALSE` for producing data for anything else downstream ...
written 16 hours ago by
Kevin Blighe ♦ 59k
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... Before we become completely confused here, which data have you downloaded? It has been implied that you have both HT-seq and RSEM data, but these are produced from different methods. Only the HT-seq files will contain a raw count, whereas RSEM files will contain an estimated count. If you literally ...
written 18 hours ago by
Kevin Blighe ♦ 59k
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