What's going on with Brad Penny using PFX?
Well we know what's going on with him as he was put on the DL with shoulder inflammation again. But what effect was that having on his pitching? Was the inflammation truly causing him to lose control? Was it making him more hittable? Looking at the data, if this is a true reflection of how shoulder inflammation manifests itself, we might have to look at certain statistics differently. I took a look at all of the pitches thrown within the last 90 days.
Penny has been on the DL twice now this season alone for inflammation in his shoulder. 
When he returned from the DL last time, his end speed just was not at the same level as it was before he went on the DL the last time averaging about 3-5 MPH less than what it was before the DL the first time. It's important to compare pitch speeds within each group and the drop-off is pretty dramatic. To me this says that he clearly wasn't fully healthy when he returned even if he reported no pain.
Release points might be able to help show if there were any problems recently. First though, as a group it appears that he clearly releases the fastball from a different slot than he does the other pitches. Scouts and GMs everywhere want the same arm action for every pitch so that
The charts clearly show how those are more skewed towards the right (towards 0) on the x-axis. What I found interesting though was that there wasn't as much of a vertical difference between the starts as I expected. With that being said, a range of a foot in terms of release point is quite a large distance. Ideally it should be equal across everything the board, but realistically you want to get the difference closer to a range of 2 baseball widths or 6". The same goes for the horizontal axis and here you can really notice a large difference. This horizontal measurement is much more effected by factors such as where the pitcher is standing on the rubber which can lead to a difference of several inches as well. In these two charts, he appears to be in these parameters. He definitely tends to release his fastball differently from his other pitches.
But we're mainly focusing on the vertical release point. The last chart is very telling. As the game goes on his vertical release point lowers dramatically especially after the 5th inning. While I expect that a decrease in release point height is normal for all pitchers, seeing that dramatic a change is telling. To me the inflammation is due mostly caused by fatigue and not necessarily a new mechanical disruption of the muscle fibers (strains). This can also go hand in hand with the finding that his average end speed is lower now than before. Note: The problem is that if he had a minor tear in his shoulder prior to this year, the difference would not be seen as much within this year.
Looking at his movement next, I don't see anything that really sticks out to me initially.
Looking at the second chart though we start to see a general trend showing fatigue setting in fairly early. His pitches start to lose movement as early as the 2nd inning. Usually if a pitcher is healthy fatigue doesn't set in this early, which makes me worried and curious. There are many injuries which can cause early fatigue including over-training (overworking), labrum pathology, rotator cuff pathology, or general laxity in the shoulder.
The next two charts show the result of the pitches:
These results don't show anything that really jump out to me. The % of pitches that are thrown for balls, strikes and those that are hit in play stay roughly constant throughout the times, except for immediately. It seems though that the rates stay roughly constant except for 3 main events. Balls in play with outs recorded are very far down in each of the starts leading up to being put on the DL. Also the amount of pitches that were balls increased while the pitches for strikes decreased. This is what I expected.
I think that while we are too far away from being able to diagnose what is wrong, but I think that we will be able to tell if something is wrong. From these I think we can be fairly certain that his shoulder never recovered during his initial DL stay. Until we can get these measurements back to normal, I would worry about a recurrence.
