Monday, March 31, 2025

omicsGMF - Why I'm going to have to install R Studio on my new laptop...

 


You know - I was really pumped when my kid's puppy was like "HEY HEY HEY GUY I HATE, WAKE UP OR I'M ABSOLUTELY GOING TO TAKE A DUMP IN YOUR APARTMENT!!" 

So we walked in the pouring rain without either of our coats until she found the absolute perfect place to poop about 3 blocks from our apartment at 4am. 

And then my Inbox was like - "HEY HEY HEY GUESS WHAT! YOU'RE GOING TO HAVE TO TOTALLY INSTALL R STUDIO ON YOUR PERFECTLY OKAY NEW LAPTOP!" 

And here is why I have to stop putting it off....


I don't have an accessible (free) solution for large scale batch effect correction right now. Do you? I guess I can MSStats it, but a long time ago I realized I'm probably just not smart enough to use it. omicsGMF does require me to fire up R which I do have an official certificate saying that I took a bunch of classes in. But it looks to me like I don't have to think about it after I do. It looks like it is smart enough to apply the corrections if I just get everything formatted the right way. 

Now - the upside is that as long as I don't try to rollerblade to work today (Pittsburgh pavement is tough to predict when it's wet) my day absolutely has to get better! 

https://github.com/statOmics/GMFProteomicsPaper

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