Dear all, I am currently determining copynumber regions for tumor cell lines using GLAD as model for the SNP6.0 array. (This takes about 13 hrs per array and per cluster node)
My problem is the interpretation of the results. Here are some examples: 1. example: "chromosome" "start" "stop" "mean" "count" "call" 1 3674045 10539859 0.154251128612596 4517 "neutral" 1 10544961 10544961 1.57871123504559 1 "gain" 1 10546623 10546623 -2.21390332082091 1 "loss" 1 10548849 21751915 0.150400582947561 6872 "neutral" This example has two regions where start=stop position (10544961, 10546623). How do you interpret this result? How should regions with count=1 be interpreted? Are these two regions considered to be outliers? 2. example: "chromosome" "start" "stop" "mean" "count" "call" 6 18253390 18253886 -1.33576824261601 2 "loss" 6 18254264 29945167 -0.0986937482773974 7921 "neutral" 6 29945167 29945167 1.47894372023 1 "gain" 6 29945294 30015940 0.225347608366043 42 "gain" Here you see two regions with different start positions but identical stop positions (=29945167), where one region shows a gain but the other region is neutral. How do you interpret this result? 3. example: "chromosome" "start" "stop" "mean" "count" "call" 8 15672606 15672655 -2.45103201175721 2 "loss" 8 15672695 15672695 -4.68547262667068 1 "loss" 8 15672695 15678118 -2.65573944523429 10 "loss" 8 15678687 15678880 -2.01991964356680 3 "loss" In this case two regions have identical start positions (=15672695). How can this be the case? Could this be a bug, since it is assumed that two regions should not overlap? 4. example: "chromosome" "start" "stop" "mean" "count" "call" 17 23813398 32995436 -0.272936124639797 5529 "neutral" 17 32999012 32999012 -2.26635873379834 1 "loss" 17 32999012 32999012 -8.28862000630996 1 "loss" 17 33000940 36676630 -0.295688057544771 1841 "neutral" This example seems to be a combination of examples 2 and 3: Here you have two identical regions with identical positions and start=stop (=32999012) How can two regions be identical but show a different mean (-2.266 vs -8.288)? Could this be a bug? In summary my questions are: How should I interpret the results? Would it be better to eliminate these regions? Thank you in advance. Best regards Christian --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
