some questions with msstats

[Dezi Tse]

HI,

I finshed TMT 2 plex experiments. Can I use msstats drew heatmap or volcano with tmt datas?

If it is allowed, what should I write in IsotopeLabelType raw?

Thank you!

[ting huang]

Yes, you can. Assuming data.res is the output from groupComparisonTMT(), try the following code:

 libarary(MSstats)

 ## profile plot

  data.res$Tvalue <-data.res$log2FC/data.res$SE

  groupComparisonPlots(data=data.res, type="VolcanoPlot", FCcutoff = 2,

                       logBase.pvalue=2)

  # Comparison Plot

  groupComparisonPlots(data=data.res, type="ComparisonPlot")

[Dezi Tse]

Hi

I have got ComparisonPlpot and volcano plot. I try to writie a heatmap. Can I do that?

Thank you!

[ting huang]

Yes, you can use the same function but change the type to Heatmap.

 libarary(MSstats)

 ## Heatmap of adjusted p-values for multiple comparisons

  data.res$Tvalue <-data.res$log2FC/data.res$SE

  groupComparisonPlots(data=data.res, type="Heatmap", FCcutoff = 2,

                       logBase.pvalue=2)

[Dezi Tse]

Hi，

I used the code but it shows :

Error in groupComparisonPlots(data = test.contrast, type = "Heatmap",  : 

  At least two comparisons are needed for heatmaps.

How to fix it?  Are positive and negative two comparisons? I have 6 positive groups and 6 negative groups.

Thank you!

[ting huang]

If the code works for volcano plot, it should be also fine for heatmap. Could you share your testing results (test.contrast)?

Best,

Ting

[Dezi Tse]

Of course.

Thanks a lot.

[ting huang]

It seems that heatmap function from MSstats is not applicable to your data. Because heatmaps in MSstats require at least two comparisons but your data has only one comparison (ACO-HA). The heatmaps in MSstats is to illustrate up-/down-regulated proteins for multiple comparisons with all proteins. Each row represents each protein. Each column represents each comparison of interest. So it needs at least two columns (two comparisons).