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Recent Replies
Comment: Is a log2 transformation an essential step in preparing expression data for mach
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ATpoint
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You're shooting buzz words as in the question before. Please read the underlying literature and follow guided tutorials. There is no genera…
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ATpoint
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Please show the functions to calculate this. Both transformations are simple division and multiplication operations with the column sums of…
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Sib
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Sorry, is log2 taransformation also needed? Or we can apply ML methods on expression data without it?
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I don't have a better mathematical explanation, but FPKMs are not reliable for gene expression studies, there are many discussions about t…
Comment: TPM vs FPKM divergence at high values
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megancgrdnr
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Thank you for your answer! Do you have any sense of why the expression values diverge at higher-expressed genes? I can't see anything in th…
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GCSA indexing certainly can be time consuming. On a reasonably well-behaved graph (such as those derived from VCFs, or usually those from t…
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There are too few valid genes in the input matrix expr_filtered, possibly because after the goodSamplesGenes filtering, only the grey modul…
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please read this paper:
[ComBat-seq][1]
[1]: https://academic.oup.com/nargab/article/2/3/lqaa078/5909519
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I asked the same question months ago...
[https://www.biostars.org/p/9604385/][1]
[1]: https://www.biostars.org/p/9604385/
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Go with TPM, when you use TPM, the sum of all TPMs in each sample are the same. This makes it easier to compare the proportion of reads tha…
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Thank you for your reply, but when I tried to log in to ANVIL, I was told that I didn't have access, so I tried to ask for help.
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Check this out: [Biorixv][1]
[1]: https://www.biorxiv.org/content/10.1101/2024.08.18.608522v1.full
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