Molly Davis added a comment - 13/Dec/23 11:04 AM - edited Questions to keep in mind : Why are the axis not all the same for each volcano plot?: We decided to not make the axis all of the same for each volcano plot because we were concerned that there would be a fitting issue. Some genes could become cut out or if the axis are too large you wouldn't be able to see the trend for that comparison. Do we want to change the x -axis to 10 for example and the y-axis to 100 because that is the highest numbers out of all of the volcano plots? I believe the change would make the volcano shape unrecognizable if we did that. To prove this I actually changed the xlim to 'xlim = c(-10, 10)' and ylim to 'ylim = c(0,50)'. These are the results and plots if we were to do that: Y-axis changed to 50: FindControlVsStressDEGenes-SL4-DESeq2.pdf Why is the log-pvalue negative on the y-axis?: Volcano plot y-axes are the negative log (base 10) of the nominal (unadjusted) p value. The horizontal lines show the p value corresponding to the input nominal p value that, when adjusted, yields a value equal to the FDR (Q) cutoff used to decide differential expression. Do we need to change all the axis to be the same and would it really make a difference for each comparison? Every single volcano plot has their own statistical analysis due to the data being pulled out for each one. For example, 'are genotype comparison 28 vs 34 at 75 min' only includes 'are' data at 75 min. for both temperatures. The analysis is only taking into account the temperature for the analysis. We parsed out the time so that the analysis was also clear about each time point but time is not a factor in the analysis. Would it actually be necessary to make all of the axis the same even though we are separately identifying genes for each genotype? Important Note : In the paper, Figure 9 shows old volcano plots that do not have the x-axis as a set (-10,10) but you can see in the new volcano plots that were added to the Supplamental data, do have the (-10,10) set for the x-axis. The y-axis was not changed because it would pancake the other volcano plots.

Molly Davis added a comment - 13/Dec/23 3:13 PM - edited Reviewer : Please go over how the questions above were answered and please make comments or edits if needed. Review the new FindControlVsStressDEGenes-SL4-DESeq2.pdf file (see previous comment) and find the volcano plots in the file to review the new set axis' that were made for each plot and make comments of if we should or shouldn't change the axis. The axis' should be (0,50) for the y-axis and (-10,10) for the x-axis. Robert Reid

Robert Reid added a comment - 14/Dec/23 10:12 AM Why are the axis not all the same for each volcano plot? I would also add that one purpose of a volcano is to show the general "volcano" like appearance that is usually observed in datasets like this. If we scale to the max value on the Y-axis, some of these plots will collapse visually. It's a trade off! Why is the log-pvalue negative on the y-axis?: GREAT ANSWER !! Do we need to change all the axis to be the same and would it really make a difference for each comparison? It makes no difference to the results. And it hampers the visual impact, losing potential details that can be seen in the plot. We can however make a note in the legend that the scales on the Y-axis change for each plot, as a reminder to the reader!

Robert Reid added a comment - 14/Dec/23 10:33 AM - edited Looking at the PDF next.......

Molly Davis added a comment - 14/Dec/23 12:13 PM - edited Meeting Notes : Fix the custom volcano plots to have a x-axis min max of (-10,10) Change the colors of all of the volcano plots to have more saturated colors of blue and red. Then make the middle grey instead of black. Change the negative log value y-axis to have a max of 20 after being transformed

Molly Davis added a comment - 14/Dec/23 4:55 PM Next step : Make new tickets for code changes. This would include one for colors with x-axis and then another ticket for the y-axis ceiling code changes. Then move this ticket to done!