Dear All, I would like to know the difference between the column Detection pvalue in the illumina file and the output of the Detection function in the Lumi package, it is the same?? Illumina file ProbeID TragetID X3.20987.AVG_Signal X3.20987.Detection.Pval X3.20987.NARRAYS X3.20987.ARRAY_STDEV 6450255 7A5 31.7491 0.6429513 1 Non Numérique 2570615 A1BG 36.09774 0.2358366 1 Non Numérique 6370619 A1BG 33.89769 0.4202898 1 Non Numérique 2600039 A1CF 37.17828 0.1752306 1 Non Numérique 2650615 A1CF 34.7686 0.3346508 1 Non Numérique 5340672 A1CF 34.63847 0.345191 1 Non Numérique 1090041 A26A1 36.3066 0.2213439 1 Non Numérique 6380561 A26A1 31.2577 0.6956522 1 Non Numérique 7570255 A26B1 31.36052 0.6824769 1 Non Numérique 4920477 A26C1B 33.63959 0.4453228 1 Non Numérique 2000519 A26C3 38.91051 0.1172596 1 Non Numérique 3870044 A26C3 27.10599 0.9657444 1 Non Numérique 7050209 A26C3 34.83817 0.3280632 1 Non Numérique 1580181 A2BP1 29.32708 0.8524374 1 Non Numérique Output of Detection function using lumi package detect <- detection(x.lumi) detect[1:5,1:5] X3.20987 X3.21585 X3.21712 X3.21759 X3.22075 6450255 0.3570487 0.6837945 0.4637681 0.2200264 0.1844532 2570615 0.7641634 0.8339921 0.8801054 0.8524374 0.8774704 6370619 0.5797102 0.9341238 0.4189723 0.2753623 0.9038208 2600039 0.8247694 0.8181818 0.1857708 0.3781291 0.5454545 2650615 0.6653492 0.7786561 0.7523057 0.7140975 0.2279315 Any help would be greatly appreciated. Thank you, Mohamed Lajnef [[alternative HTML version deleted]]