Recently I ran a WGCNA network construction analysis. The array type has more than 50K genes but luckily I have a powerful cluster which has more than 600G memory, so I set the maxBlockSize=60000. But I got the error message: 'maxBlockSize must be less than 46340. Please decrease it and try again.' Where does this 46340 come frome? Can I use any size of maxBlockSize if I have enough memory? I have also posted this question on biostars but didn't get an answer yet. Thank you. -Xiaokuan

The limit is (the square root of) the maximum matrix size addressable by a 4-byte pointer. I will eventually update the WGCNA code to remove the limit, but for now it is what it is. The limit is independent of how much memory you have. Sorry!

Peter