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Originally Posted by van19
it doesnt include all parts like ... cpu cooling
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The heatsink that comes with the factory PC will almost definitely be your CPU's stock one. This comes included with the CPU when you buy from any computer store like NCIX.
Factory PCs will be cheaper on the low-performance end of computing (e.g. Dell's $299-399 PCs), but once you start getting into the high performance territory, where PSUs, heatsinks, and mobos actually matter, the custom build PC will be cheaper, but you'll have to put in more effort to find good price matches and sales.
My current PC (2 weeks old) cost me $878 after taxes at NCIX. I couldn't find anything cheaper at Dell, and I'm sure that I have a better mobo (USB 3.0/SATA 6GB), PSU, CPU heat sink, and case than anything any of the big box companies could offer.