Molly Davis added a comment - 10/Nov/23 11:21 AM - edited Update : Last time we spoke we have been working on two requests. The first was fixing the bug in the 'FindMutantVsWildtypeDEGenes-DESeq2.Rmd' markdown. The issue was in a data frame that showed counts of significant genes with an adjusted pvalue of less than or equal to 0.01 and a lfcThreshold of greater than or equal to 1. The issue with this is that it did not include the lfcThreshold of less than or equal to -1, so the counts were not correct in the data frame. To fix this we added an absolute value function, abs(), that include the -1 and 1 values for the lfcThreshold. The table should now include higher amounts of significant genes. Bug fixed Files : Markdown: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/FindMutantVsWildtypeDEGenes-DESeq2.Rmd Knitted PDF: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/FindMutantVsWildtypeDEGenes-DESeq2.pdf The second update is a new markdown that creates the custom volcano plots that were requested. This included plots displaying the temperature dependent DE genes from the final timepoints (75min) for each genotype, without gene IDs on the plot. The method was DESeq2 and the SL4 genes names were used. Custom Volcano Plot Files : Markdown: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/MakeCustomVolcanoPlots.Rmd Knitted PDF: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/MakeCustomVolcanoPlots.pdf Volcano Plots PDF: https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/CustomVolcanoPlots-SL4-DeSeq2.pdf If you have any questions or more requests let us know! Thank you!

Ann Loraine added a comment - 10/Nov/23 2:07 PM This sounds great! Moving to DONE.