Moderator: igor

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igor10k
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Posts by igor

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Comment: C: Very low probability densities
... Why do you think they are low? Your chromosome has millions of bases, but you only have values for about a thousand of them. In other words, most values are 0, so the average should be very low. ...
written 6 hours ago by igor10k
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Answer: A: retrieve TPM matrix from raw counts matrix or DESeq2 object dds
... > So is it possible to get TPM or even FPKM matrix from raw count martix? DESeq2 has the `fpkm()` function specifically for that. If you just want TPMs and keep things simple, you could also just download them from [Xena][1]. [1]: https://xenabrowser.net/datapages/?host=https%3A%2F%2Ftoil.x ...
written 23 hours ago by igor10k
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Comment: C: KEGG pathway gene lists differ between sources
... You can try [KEGGgraph][1], which downloads directly from KEGG, so you end up with the current version. [1]: https://www.bioconductor.org/packages/release/bioc/html/KEGGgraph.html ...
written 1 day ago by igor10k
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Comment: C: remove Batch Effect between several **RNA-seq** studies (no replication)
... If you cannot remove that study, does it mean it has information that the other studies don't? In that case, that study has 2 different variables (that and the batch), so you don't know how much each is contributing. ...
written 2 days ago by igor10k
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Comment: C: Using limma for scRNAseq data
... You could also treat the replicates as a covariate. ...
written 2 days ago by igor10k
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Comment: C: remove Batch Effect between several **RNA-seq** studies (no replication)
... If that one study is very important and you cannot remove it, then how can you comment on or correct the batch effect? There is only a single batch. ...
written 2 days ago by igor10k
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Comment: C: GSEA with mouse RNAseq data
... MSigDB pathways are presented as human symbols, but are based on multiple species. Related discussion: https://www.biostars.org/p/147484/ ...
written 2 days ago by igor10k
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Answer: A: KEGG pathway gene lists differ between sources
... The best source for KEGG pathways should be KEGG itself. Other sources may be outdated or have some restrictions. MSigDB support forum had a nice [explanation][1]: > For the Reactome database, the information you found in the release > notes is correct - it is based on Reactome version 44. W ...
written 2 days ago by igor10k
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Comment: C: Using limma for scRNAseq data
... Maybe you don't really need to reinvent the wheel. Something like the t-test or the Wilcoxon test have been used for all sorts of data over many years. The advantage of a generic test is that it is generic. ...
written 2 days ago by igor10k
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Answer: A: Using limma for scRNAseq data
... [Soneson et al][1] compared a few different methods, including limma, so it's certainly possible: ![enter image description here][2] [1]: https://doi.org/10.1038/nmeth.4612 [2]: https://media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fnmeth.4612/MediaObjects/41592_2018_Art ...
written 5 days ago by igor10k

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