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This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan Albert,
New @bergmanlab preprint addressing the unsolved question:
"What is the best bioinformatic tool for calling transposable element (TE) variants in WGS data?" https://t.co/ZEMFHtf0ch
— Casey Bergman (@caseybergman) February 14, 2023
New @bergmanlab preprint addressing the unsolved question:
"What is the best bioinformatic tool for calling transposable element (TE) variants in WGS data?" https://t.co/ZEMFHtf0ch
submitted by: Istvan Albert
I agree with everything said. However, there is ANOTHER BIGGER ISSUE. The vast majority of these enrichment analysis tools are invalid to begin with (regardless of background).
All of the p-values from these tests are almost universally invalid
— Mike Wu (@mike@genomic.social) (@wu_biostat) February 17, 2023
I agree with everything said. However, there is ANOTHER BIGGER ISSUE. The vast majority of these enrichment analysis tools are invalid to begin with (regardless of background).
All of the p-values from these tests are almost universally invalid
submitted by: Istvan Albert
Urgent need for consistent standards in functional enrichment analysis | PLOS Computational Biology (journals.plos.org)
We find that 95% of analyses using over-representation tests did not implement an appropriate background gene list or did not describe this in the methods. Failure to perform p-value correction for multiple tests was identified in 43% of analyses.
submitted by: Istvan Albert
Multiple sources of bias confound functional enrichment analysis of global -omics data | Genome Biology | Full Text (genomebiology.biomedcentral.com)
Serious and underappreciated sources of bias mean that extreme caution should be applied when using or interpreting functional enrichment analysis to validate findings from global RNA- or protein-expression analyses.
submitted by: Istvan Albert
I want to talk today about a methodological issue in #genomics research that has been around a long time but is still a major problem.
The reason is that today I reviewed another manuscript that has this exact problem.
— Mark Ziemann🌈🌻 (@mdziemann) February 17, 2023
I want to talk today about a methodological issue in #genomics research that has been around a long time but is still a major problem.
The reason is that today I reviewed another manuscript that has this exact problem.
submitted by: Istvan Albert
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