More descriptive axis labels for the MA plot

[fabianegli]

The MA plot axis labels are quite cryptic for unexperienced users.

[wolski]

Agreed that it could be improved. Could you help me choose a better Axis labels for X and Y

"M" and "A" "log fold change" and "mean expression" "log fold change" and "normalized mean expression" But what if a different normalization e.g. "asinh", is used? or for consistency "c1- c2" and "(c1+c2)/2"

"normalized fold change" and "normalized mean expression"

or maybe, if I would use the names of the contrasts i could generate something like "Treatment - Control" vs "Treatment + Control" but this would be harder to implement.

[fabianegli]

Hard to say what's best, since the data is not always the same.

I see three possible solutions:

• supply the labels when calling the ma_plot function
• have the data supplied to the ma_plot function bring along the labels
• hardcoding the labels

Since the data might be changing, it might be a good idea to use something generic as default, like "change" and "average", but I see that a valid approach would also be to use the "original" axis labels: "logged intensity ratio (M)" and "mean logged intensities (A)" (have no clue "how" original that actually is, if at all).

... or another example from Experimental Design and Analysis of Microarray Data Claire H. Wilson: "M = log2 (Fold Change)" and "A = log2 (Average Intensity)"

[wolski]

Hello @fabianegli ,

I decided to go with your suggestion "logged intensity ratio (M)" and "mean logged intensities (A)". See commit: https://github.com/wolski/prolfqua/commit/87b00f642490f451e13e8a4828bf9f96697d2681

Thanks for your help.

[fabianegli]

Great, glad to hear and that it was of help.