怎样进行根本原因分析?

本月我公司进行认证,提出问题如下:现要求填写纠正报告,请教各位:如何进行从系统或流程上进行原因分析:
不符合项如下:
1.7.3.3.2The PFMEA process is not effective: For the PFMEA2003001A of product ,the hole drill, no process changed ,but the occour index changed from 5 to 3.(TSonly)
2.The product development outputs is not effective, 1) in the PFMEA , some process defined on the process flow chart are miss, 2) in the control plan, some evaluation and measurment technics are not identified, e.g, clip space.
3.The monitoring of the project measurements at development phase is not effective, in various gate of the development of the project , there is no evidence that the cost and quality risks has monitored and report to top management as the management review inputs.
4.7.4.1The purchasing process is not effective:1. the supplier poor quality because of bad packing in July, but no evidence that any analysis and actions was conducted on this issue. 2.Emergency purchasing in Jun. Sept. and Nov., but also no any analysis and actions.