Question: doubt in HTqPCR
0
gravatar for Heidi Dvinge
8.1 years ago by
Heidi Dvinge2.0k
Heidi Dvinge2.0k wrote:
Madam, > Sir, > > Iam afraid that whether in R HTqPCR iam getting inconsistent results with > same sets of data. I have analysed same data got two different results > details of analysis and results that is given below. In both i have used > same data only difference in file.txt, in analysis1 the all normal sample > are cluster together and analysis 2 are randomly arranged. > It looks like your problem is that you don't start with a clean workspace. When you start R you should notice the line: > [Previously saved workspace restored] I.e. you ahve some old objects floating around. WHen you read in file.txt you assign it to the object "exFiles", but when you run the analysis you say "groups=files$Treatment[1:99]". The object "files" has nothing whatsover to do with your file.txt, but seems to be something left over from a previous analysis. Try starting from a clean workspace, or start out with typing rm(list=ls()). HTH \Heidi > > > Analysis 1 > > > > R version 2.11.0 (2010-04-22) > > Copyright (C) 2010 The R Foundation for Statistical Computing > > ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > > You are welcome to redistribute it under certain conditions. > > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > > Type 'contributors()' for more information and > > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > > 'help.start()' for an HTML browser interface to help. > > Type 'q()' to quit R. > > [Previously saved workspace restored] > >> library(HTqPCR) > > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > > 'openVignette()'. To cite Bioconductor, see > > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: RColorBrewer > > Loading required package: limma > >> library(limma) > >> library(RColorBrewer) > >> exPath <- "F:/HTqPCR/tlda_new_all" > >> exFiles <- read.delim(file.path(exPath, "files.txt")) > >> raw <- readCtData(files=exFiles$File[c(1:99)], path=exPath, n.features = > 48, flag = 4, feature = 6, type = 7, position = 3, Ct = 8, header = FALSE, > SDS = FALSE, n.data = 1, na.value = 40) > >> raw > > An object of class "qPCRset" > > Size: 48 features, 99 samples > > Feature types: Endogenous Control, Target > > Feature names: CCNF-Hs00171049_m1 RBL2-Hs00180562_m1 > CCND1-Hs00277039_m1 ... > > Feature classes: > > Feature categories: OK, Undetermined > > Sample names: N1 N2 N3 ... > >> path <- "F:/HTqPCR/tlda_new_all" > >> (read.delim(file.path(path, "files.txt"))) > > File Treatment > > 1 N1.txt Normal > > 2 N2.txt Normal > > 3 N3.txt Normal > > 4 N4.txt Normal > > 5 N5.txt Normal > > 6 N6.txt Normal > > 7 N7.txt Normal > > 8 N8.txt Normal > > 9 N9.txt Normal > > 10 N10.txt Normal > > 11 N11.txt Normal > > 12 N12.txt Normal > > 13 N13.txt Normal > > 14 N14.txt Normal > > 15 N15.txt Normal > > 16 N16.txt Normal > > 17 N17.txt Normal > > 18 N18.txt Normal > > 19 N19.txt Normal > > 20 N20.txt Normal > > 21 N21.txt Normal > > 22 N22.txt Normal > > 23 N23.txt Normal > > 24 N24.txt Normal > > 25 T1.txt tumor > > 26 T2.txt tumor > > 27 T3.txt tumor > > 28 T4.txt tumor > > 29 T5.txt tumor > > 30 T6.txt Normal > > 31 T7.txt Normal > > 32 T8.txt tumor > > 33 T9.txt tumor > > 34 T10.txt tumor > > 35 T11.txt tumor > > 36 T12.txt tumor > > 37 T13.txt tumor > > 38 T14.txt tumor > > 39 T15.txt tumor > > 40 T16.txt tumor > > 41 T17.txt tumor > > 42 T18.txt tumor > > 43 T19.txt tumor > > 44 T20.txt tumor > > 45 T21.txt tumor > > 46 T22.txt tumor > > 47 T23.txt tumor > > 48 T24.txt tumor > > 49 T25.txt tumor > > 50 T26.txt tumor > > 51 T27.txt tumor > > 52 T28.txt tumor > > 53 T29.txt tumor > > 54 T30.txt tumor > > 55 T31.txt tumor > > 56 T32.txt tumor > > 57 T33.txt tumor > > 58 T34.txt tumor > > 59 T35.txt tumor > > 60 T36.txt tumor > > 61 T37.txt tumor > > 62 T38.txt tumor > > 63 T39.txt tumor > > 64 T40.txt tumor > > 65 T41.txt tumor > > 66 T42.txt tumor > > 67 T43.txt tumor > > 68 T44.txt tumor > > 69 T45.txt tumor > > 70 T46.txt tumor > > 71 T47.txt tumor > > 72 T48.txt tumor > > 73 T49.txt tumor > > 74 T50.txt tumor > > 75 T51.txt tumor > > 76 T52.txt tumor > > 77 T53.txt tumor > > 78 T54.txt tumor > > 79 T55.txt tumor > > 80 T56.txt tumor > > 81 T57.txt tumor > > 82 T58.txt tumor > > 83 T59.txt tumor > > 84 T60.txt tumor > > 85 T61.txt tumor > > 86 T62.txt tumor > > 87 T63.txt tumor > > 88 T64.txt tumor > > 89 T65.txt tumor > > 90 T66.txt tumor > > 91 T67.txt tumor > > 92 T68.txt tumor > > 93 T69.txt tumor > > 94 T70.txt tumor > > 95 T71.txt tumor > > 96 T72.txt tumor > > 97 T73.txt tumor > > 98 T74.txt tumor > > 99 T75.txt tumor > >> raw.cat <- setCategory(raw, Ct.max = 38, Ct.min = 5, replicates = TRUE, > quantile = NULL, groups, flag = TRUE, flag.out = "Failed", verbose = TRUE, > plot = FALSE) > > Categories after Ct.max and Ct.min filtering: > > N1 N2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 N15 N16 N17 > N18 > N19 > > OK 48 48 47 46 48 48 48 48 48 48 48 47 48 48 48 48 43 > 48 > 48 > > Undetermined 0 0 1 2 0 0 0 0 0 0 0 1 0 0 0 0 5 > 0 > 0 > > N20 N21 N22 N23 N24 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 > T13 > T14 > > OK 48 47 48 3 48 48 48 48 48 48 48 48 46 48 48 48 48 > 48 > 48 > > Undetermined 0 1 0 45 0 0 0 0 0 0 0 0 2 0 0 0 0 > 0 > 0 > > T15 T16 T17 T18 T19 T20 T21 T22 T23 T24 T25 T26 T27 T28 T29 > T30 > > OK 48 48 48 48 48 48 44 48 45 48 48 48 48 48 48 > 48 > > Undetermined 0 0 0 0 0 0 4 0 3 0 0 0 0 0 0 > 0 > > T31 T32 T33 T34 T35 T36 T37 T38 T39 T40 T41 T42 T43 T44 T45 > T46 > > OK 48 48 48 48 48 48 48 48 48 48 48 48 48 48 48 > 48 > > Undetermined 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 > > T47 T48 T49 T50 T51 T52 T53 T54 T55 T56 T57 T58 T59 T60 T61 > T62 > > OK 47 48 48 48 48 48 48 48 48 48 48 48 48 48 48 > 48 > > Undetermined 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 > > T63 T64 T65 T66 T67 T68 T69 T70 T71 T72 T73 T74 T75 > > OK 48 48 48 48 48 48 34 33 21 47 47 46 46 > > Undetermined 0 0 0 0 0 0 14 15 27 1 1 2 2 > >> q.norm <- normalizeCtDataraw.cat, norm="quantile") > >> qDE.ttest <- ttestCtData(q.norm[,1:99], groups=files$Treatment[1:99], > > + calibrator="Normal") > >> qDE.ttest[1:48,] > > genes feature.pos t.test p.value adj.p.value > > 47 TP53-Hs00153349_m1 M5 2.295891791 0.02812777 0.7125000 > > 31 CDKN2A-Hs00233365_m1 N9 -2.082255233 0.04380924 0.7125000 > > 2 ATM-Hs00175892_m1 N23 1.937805071 0.06000455 0.7125000 > > 4 BCL2-Hs00608023_m1 N24 1.770657925 0.08396548 0.7125000 > > 24 CDK5-Hs00358991_g1 N5 -1.666016360 0.10350732 0.7125000 > > 20 CDC25C-Hs00156411_m1 M12 1.630183670 0.10933804 0.7125000 > > 27 CDK8-Hs00176209_m1 M14 -1.546067079 0.12925207 0.7125000 > > 46 TGFA-Hs00608187_m1 N22 -1.547216622 0.12962975 0.7125000 > > 36 E2F1-Hs00153451_m1 N13 1.496405692 0.14153371 0.7125000 > > 3 ATR-Hs00169878_m1 N16 1.424482218 0.16073293 0.7125000 > > 33 CDKN2C-Hs00176227_m1 N15 1.329395172 0.19193228 0.7125000 > > 1 18S-Hs99999901_s1 M11 1.330427353 0.19295059 0.7125000 > > 14 CCNF-Hs00171049_m1 M1 -1.264650510 0.21288347 0.7125000 > > 25 CDK6-Hs00608037_m1 M13 -1.260494621 0.21591150 0.7125000 > > 29 CDKN1B-Hs00153277_m1 M20 1.197283433 0.23807788 0.7125000 > > 9 CCND1-Hs00277039_m1 M3 1.186232786 0.24153101 0.7125000 > > 16 CCNH-Hs00236923_m1 M18 1.159827899 0.25234377 0.7125000 > > 42 PIN1-Hs00749260_s1 M7 -1.017033208 0.31677086 0.7312508 > > 44 RBL1-Hs00765707_m1 N6 -0.990603791 0.32746372 0.7312508 > > 35 CHEK1-Hs00176236_m1 M4 -0.984312292 0.32974562 0.7312508 > > 22 CDK2-Hs00608082_m1 N7 0.921231845 0.36229801 0.7312508 > > 19 CDC20-Hs00415851_g1 N20 -0.891251276 0.37816127 0.7312508 > > 30 CDKN1C-Hs00175938_m1 N17 0.885721819 0.38133275 0.7312508 > > 23 CDK4-Hs00364847_m1 M10 0.880593383 0.38332999 0.7312508 > > 38 EGFR-Hs00193306_m1 M6 -0.861446299 0.39248804 0.7312508 > > 48 TP53BP2-Hs00610488_m1 M17 -0.859232889 0.39609417 0.7312508 > > 26 CDK7-Hs00757090_g1 N8 -0.793062156 0.43214696 0.7682613 > > 8 CCNC-Hs00193177_m1 M8 -0.748176629 0.46024346 0.7780245 > > 39 GADD45A-Hs00169255_m1 N4 0.730384641 0.47005649 0.7780245 > > 12 CCNE1-Hs00233356_m1 N11 -0.661190280 0.51247743 0.8199639 > > 40 MDM2-Hs00242813_m1 N14 0.523011580 0.60315433 0.9162412 > > 32 CDKN2B-Hs00793225_m1 M16 -0.511063425 0.61082746 0.9162412 > > 18 CDC2-Hs00364293_m1 N21 0.424545098 0.67372768 0.9398924 > > 6 CCNB1-Hs00259126_m1 M23 -0.397648195 0.69294867 0.9398924 > > 43 RB1-Hs00153108_m1 M24 -0.356106465 0.72438495 0.9398924 > > 21 CDC34-Hs00362082_m1 M9 -0.347115072 0.73067318 0.9398924 > > 7 CCNB2-Hs00270424_m1 N19 0.343158811 0.73340270 0.9398924 > > 45 RBL2-Hs00180562_m1 M2 0.301231001 0.76499875 0.9398924 > > 37 E2F2-Hs00231667_m1 N12 0.264437309 0.79257682 0.9398924 > > 17 CCNK-Hs00395018_m1 N2 0.250846802 0.80298088 0.9398924 > > 41 MKI67-Hs00606991_m1 M19 -0.221244374 0.82592897 0.9398924 > > 13 CCNE2-Hs00180319_m1 N18 0.207823187 0.83649945 0.9398924 > > 34 CDKN2D-Hs00176481_m1 N10 -0.200743474 0.84198691 0.9398924 > > 11 CCND3-Hs00426901_m1 M15 -0.136550193 0.89195280 0.9511576 > > 15 CCNG2-Hs00171119_m1 M21 0.124235792 0.90172251 0.9511576 > > 28 CDKN1A-Hs00355782_m1 N3 0.111822460 0.91152601 0.9511576 > > 5 CCNA1-Hs00171105_m1 M22 -0.051450616 0.95924075 0.9796501 > > 10 CCND2-Hs00277041_m1 N1 0.001033206 0.99918012 0.9991801 > > ddCt FC meanCalibrator meanTarget categoryTarget > > 47 -0.5771835615 1.4919338 28.29557 27.71839 Undetermined > > 31 1.2149986166 0.4307735 26.10425 27.31925 Undetermined > > 2 -0.4342070891 1.3511680 29.73063 29.29643 Undetermined > > 4 -0.7067142098 1.6320828 30.29411 29.58740 Undetermined > > 24 0.2932291238 0.8160734 27.90855 28.20178 Undetermined > > 20 -0.3931802780 1.3132852 32.55413 32.16095 Undetermined > > 27 0.2315856136 0.8516983 27.81600 28.04759 Undetermined > > 46 0.5136423509 0.7004518 26.83748 27.35112 Undetermined > > 36 -0.3443487024 1.2695777 29.15093 28.80658 Undetermined > > 3 -0.2234603706 1.1675306 28.68034 28.45687 Undetermined > > 33 -0.4275325781 1.3449314 30.19377 29.76624 Undetermined > > 1 -1.5299479008 2.8877541 11.84900 10.31905 OK > > 14 NA NA NA 27.57528 Undetermined > > 25 0.2203066750 0.8583829 26.65416 26.87446 Undetermined > > 29 -0.2577058577 1.1955760 26.47668 26.21897 Undetermined > > 9 -0.3473309551 1.2722048 26.85627 26.50894 Undetermined > > 16 -0.1645688561 1.1208311 28.09055 27.92598 Undetermined > > 42 NA NA 22.82325 NA OK > > 44 0.1898566073 0.8766929 28.86255 29.05241 Undetermined > > 35 0.1946000847 0.8738151 28.21858 28.41318 Undetermined > > 22 -0.1650715778 1.1212217 29.11399 28.94892 Undetermined > > 19 0.3223268749 0.7997789 26.74567 27.06800 Undetermined > > 30 -0.5765941675 1.4913245 28.00179 27.42520 Undetermined > > 23 -0.3528688765 1.2770977 25.44603 25.09316 Undetermined > > 38 0.1870928877 0.8783739 26.18928 26.37638 Undetermined > > 48 0.1326862796 0.9121315 27.71044 27.84313 Undetermined > > 26 0.1239877900 0.9176476 28.00722 28.13121 Undetermined > > 8 0.1290736586 0.9144184 26.98845 27.11752 Undetermined > > 39 -0.1728404506 1.1272757 28.36314 28.19030 Undetermined > > 12 0.1829117466 0.8809233 29.45615 29.63906 Undetermined > > 40 -0.1034057465 1.0743066 26.39775 26.29434 Undetermined > > 32 NA NA 27.81330 NA Undetermined > > 18 -0.0869243673 1.0621035 28.34943 28.26251 Undetermined > > 6 0.0906105280 0.9391252 28.06654 28.15715 Undetermined > > 43 0.0968366238 0.9350811 27.29783 27.39467 Undetermined > > 21 0.0659027358 0.9553473 26.67284 26.73874 Undetermined > > 7 -0.1037258208 1.0745449 27.63123 27.52750 Undetermined > > 45 -0.0574024676 1.0405905 27.51019 27.45279 Undetermined > > 37 -0.0947104615 1.0678511 28.89725 28.80254 Undetermined > > 17 -0.0259664431 1.0181615 26.96487 26.93890 Undetermined > > 41 0.0688651399 0.9533877 27.51280 27.58166 Undetermined > > 13 -0.0416421111 1.0292847 30.18775 30.14610 Undetermined > > 34 0.0403632814 0.9724101 28.51461 28.55498 Undetermined > > 11 0.0247566698 0.9829864 26.77960 26.80436 Undetermined > > 15 -0.0188040565 1.0131193 27.74717 27.72837 Undetermined > > 28 -0.0586069931 1.0414597 22.90229 22.84369 Undetermined > > 5 NA NA NA NA Undetermined > > 10 -0.0002114316 1.0001466 26.40150 26.40128 Undetermined > > categoryCalibrator > > 47 OK > > 31 OK > > 2 OK > > 4 Undetermined > > 24 OK > > 20 Undetermined > > 27 OK > > 46 OK > > 36 OK > > 3 OK > > 33 OK > > 1 OK > > 14 OK > > 25 OK > > 29 OK > > 9 OK > > 16 OK > > 42 OK > > 44 OK > > 35 OK > > 22 OK > > 19 OK > > 30 OK > > 23 OK > > 38 OK > > 48 OK > > 26 OK > > 8 OK > > 39 OK > > 12 OK > > 40 OK > > 32 OK > > 18 OK > > 6 OK > > 43 Undetermined > > 21 OK > > 7 OK > > 45 OK > > 37 OK > > 17 OK > > 41 OK > > 13 OK > > 34 OK > > 11 OK > > 15 OK > > 28 OK > > 5 Undetermined > > 10 OK > >> write.table(qDE.ttest, file="test20.xls", sep="\t", quote=FALSE, > row.names=FALSE) > >> sessionInfo() > > R version 2.11.0 (2010-04-22) > > x86_64-pc-mingw32 > > locale: > > [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252 > > [3] LC_MONETARY=English_India.1252 LC_NUMERIC=C > > [5] LC_TIME=English_India.1252 > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > > [1] HTqPCR_1.2.0 limma_3.4.3 RColorBrewer_1.0-2 Biobase_2.8.0 > > > loaded via a namespace (and not attached): > > [1] affy_1.26.1 affyio_1.16.0 gdata_2.8.0 > > [4] gplots_2.8.0 gtools_2.6.2 preprocessCore_1.10.0 > > > > > > > > > > Analysis 2 > > > > R version 2.11.0 (2010-04-22) > > Copyright (C) 2010 The R Foundation for Statistical Computing > > ISBN 3-900051-07-0 > > > > R is free software and comes with ABSOLUTELY NO WARRANTY. > > You are welcome to redistribute it under certain conditions. > > Type 'license()' or 'licence()' for distribution details. > > > > Natural language support but running in an English locale > > > > R is a collaborative project with many contributors. > > Type 'contributors()' for more information and > > 'citation()' on how to cite R or R packages in publications. > > > > Type 'demo()' for some demos, 'help()' for on-line help, or > > 'help.start()' for an HTML browser interface to help. > > Type 'q()' to quit R. > > > > [Previously saved workspace restored] > > > >> library(HTqPCR) > > Loading required package: Biobase > > > > Welcome to Bioconductor > > > > Vignettes contain introductory material. To view, type > > 'openVignette()'. To cite Bioconductor, see > > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > > > Loading required package: RColorBrewer > > Loading required package: limma > >> library(limma) > >> library(RColorBrewer) > >> exPath <- "F:/HTqPCR/tlda_new_all" > >> exFiles <- read.delim(file.path(exPath, "files.txt")) > >> raw <- readCtData(files=exFiles$File[c(1:99)], path=exPath, n.features = > 48, flag = 4, feature = 6, type = 7, position = 3, Ct = 8, header = FALSE, > SDS = FALSE, n.data = 1, na.value = 40) > >> raw > > An object of class "qPCRset" > > Size: 48 features, 99 samples > > Feature types: Endogenous Control, Target > > Feature names: CCNF-Hs00171049_m1 RBL2-Hs00180562_m1 > CCND1-Hs00277039_m1 ... > > Feature classes: > > Feature categories: OK, Undetermined > > Sample names: T1 T2 T3 ... > >> path <- "F:/HTqPCR/tlda_new_all" > >> (read.delim(file.path(path, "files.txt"))) > > File Treatment > > 1 T1.txt Tumor > > 2 T2.txt Tumor > > 3 T3.txt Tumor > > 4 T4.txt Tumor > > 5 T5.txt Tumor > > 6 N1.txt Normal > > 7 T6.txt Normal > > 8 T7.txt Normal > > 9 T8.txt Tumor > > 10 T9.txt Tumor > > 11 T10.txt Tumor > > 12 T11.txt Tumor > > 13 N2.txt Normal > > 14 T12.txt Tumor > > 15 T13.txt Tumor > > 16 N3.txt Normal > > 17 T14.txt Tumor > > 18 N4.txt Normal > > 19 T15.txt Tumor > > 20 T16.txt Tumor > > 21 T17.txt Tumor > > 22 N5.txt Normal > > 23 T18.txt Tumor > > 24 N6.txt Normal > > 25 N7.txt Normal > > 26 T19.txt Tumor > > 27 T20.txt Tumor > > 28 N8.txt Normal > > 29 T21.txt Tumor > > 30 T22.txt Tumor > > 31 T23.txt Tumor > > 32 N9.txt Normal > > 33 T24.txt Tumor > > 34 T25.txt Tumor > > 35 T26.txt Tumor > > 36 T27.txt Tumor > > 37 T28.txt Tumor > > 38 T29.txt Tumor > > 39 T30.txt Tumor > > 40 T31.txt Tumor > > 41 T32.txt Tumor > > 42 T33.txt Tumor > > 43 T34.txt Tumor > > 44 T35.txt Tumor > > 45 T36.txt Tumor > > 46 T37.txt Tumor > > 47 T38.txt Tumor > > 48 N10.txt Normal > > 49 T39.txt Tumor > > 50 T40.txt Tumor > > 51 T41.txt Tumor > > 52 N11.txt Normal > > 53 T42.txt Tumor > > 54 T43.txt Tumor > > 55 T44.txt Tumor > > 56 T45.txt Tumor > > 57 T46.txt Tumor > > 58 T47.txt Tumor > > 59 T48.txt Tumor > > 60 T49.txt Tumor > > 61 N12.txt Normal > > 62 T50.txt Tumor > > 63 T51.txt Tumor > > 64 N13.txt Normal > > 65 T52.txt Tumor > > 66 T53.txt Tumor > > 67 T54.txt Tumor > > 68 N14.txt Normal > > 69 T55.txt Tumor > > 70 N15.txt Normal > > 71 T56.txt Tumor > > 72 N16.txt Normal > > 73 T57.txt Tumor > > 74 T58.txt Tumor > > 75 T59.txt Tumor > > 76 N17.txt Normal > > 77 T60.txt Tumor > > 78 N18.txt Normal > > 79 T61.txt Tumor > > 80 T62.txt Tumor > > 81 T63.txt Tumor > > 82 T64.txt Tumor > > 83 T65.txt Tumor > > 84 N19.txt Normal > > 85 T66.txt Tumor > > 86 N20.txt Normal > > 87 T67.txt Tumor > > 88 N21.txt Normal > > 89 T68.txt Tumor > > 90 N22.txt Normal > > 91 T69.txt Tumor > > 92 N23.txt Normal > > 93 T70.txt Tumor > > 94 T71.txt Tumor > > 95 T72.txt Tumor > > 96 T73.txt Tumor > > 97 T74.txt Tumor > > 98 T75.txt Tumor > > 99 N24.txt Normal > >> raw.cat <- setCategory(raw, Ct.max = 38, Ct.min = 5, replicates = TRUE, > quantile = NULL, groups, flag = TRUE, flag.out = "Failed", verbose = TRUE, > plot = FALSE) > > Categories after Ct.max and Ct.min filtering: > > T1 T2 T3 T4 T5 N1 T6 T7 T8 T9 T10 T11 N2 T12 T13 N3 T14 N4 > T15 > T16 > > OK 48 48 48 48 48 48 48 48 46 48 48 48 48 48 48 47 48 46 > 48 > 48 > > Undetermined 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 1 0 2 > 0 > 0 > > T17 N5 T18 N6 N7 T19 T20 N8 T21 T22 T23 N9 T24 T25 T26 T27 > T28 > T29 > > OK 48 48 48 48 48 48 48 48 44 48 45 48 48 48 48 48 > 48 > 48 > > Undetermined 0 0 0 0 0 0 0 0 4 0 3 0 0 0 0 0 > 0 > 0 > > T30 T31 T32 T33 T34 T35 T36 T37 T38 N10 T39 T40 T41 N11 T42 > T43 > > OK 48 48 48 48 48 48 48 48 48 48 48 48 48 48 48 > 48 > > Undetermined 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 > > T44 T45 T46 T47 T48 T49 N12 T50 T51 N13 T52 T53 T54 N14 T55 > N15 > > OK 48 48 48 47 48 48 47 48 48 48 48 48 48 48 48 > 48 > > Undetermined 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 > 0 > > T56 N16 T57 T58 T59 N17 T60 N18 T61 T62 T63 T64 T65 N19 T66 > N20 > > OK 48 48 48 48 48 43 48 48 48 48 48 48 48 48 48 > 48 > > Undetermined 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 > 0 > > T67 N21 T68 N22 T69 N23 T70 T71 T72 T73 T74 T75 N24 > > OK 48 47 48 48 34 3 33 21 47 47 46 46 48 > > Undetermined 0 1 0 0 14 45 15 27 1 1 2 2 0 > >> q.norm <- normalizeCtDataraw.cat, norm="quantile") > >> qDE.ttest <- ttestCtData(q.norm[,1:99], groups=files$Treatment[1:99], > > + calibrator="Normal") > >> qDE.ttest[1:48,] > > genes feature.pos t.test p.value adj.p.value > > 6 CCNB1-Hs00259126_m1 I23 6.20160729 7.048712e-08 3.383382e-06 > > 35 CHEK1-Hs00176236_m1 I4 5.48408184 2.514510e-06 6.034823e-05 > > 46 TGFA-Hs00608187_m1 J22 5.21382975 4.743489e-06 7.589583e-05 > > 4 BCL2-Hs00608023_m1 J24 -4.65741536 2.384561e-05 2.861473e-04 > > 47 TP53-Hs00153349_m1 I5 -4.34020615 5.356469e-05 5.142210e-04 > > 25 CDK6-Hs00608037_m1 I13 4.15810415 9.191490e-05 7.092438e-04 > > 33 CDKN2C-Hs00176227_m1 J15 -4.24782850 1.034314e-04 7.092438e-04 > > 16 CCNH-Hs00236923_m1 I18 -3.88720229 2.996959e-04 1.798176e-03 > > 9 CCND1-Hs00277039_m1 I3 -3.90103610 3.929839e-04 2.095914e-03 > > 18 CDC2-Hs00364293_m1 J21 3.68357070 6.744105e-04 3.237170e-03 > > 12 CCNE1-Hs00233356_m1 J11 3.61548837 8.202665e-04 3.579345e-03 > > 29 CDKN1B-Hs00153277_m1 I20 -3.58651890 9.334087e-04 3.733635e-03 > > 30 CDKN1C-Hs00175938_m1 J17 -3.46267415 1.165720e-03 4.304198e-03 > > 45 RBL2-Hs00180562_m1 I2 -3.33108991 1.570514e-03 5.384621e-03 > > 39 GADD45A-Hs00169255_m1 J4 -3.27745675 2.135930e-03 6.834977e-03 > > 41 MKI67-Hs00606991_m1 I19 3.17081035 2.819846e-03 8.459537e-03 > > 7 CCNB2-Hs00270424_m1 J19 2.98768802 5.280899e-03 1.491077e-02 > > 27 CDK8-Hs00176209_m1 I14 -2.78622102 8.490709e-03 2.264189e-02 > > 10 CCND2-Hs00277041_m1 J1 2.52336007 1.446031e-02 3.653131e-02 > > 2 ATM-Hs00175892_m1 J23 -2.49985908 1.640807e-02 3.937937e-02 > > 19 CDC20-Hs00415851_g1 J20 2.42245447 2.076797e-02 4.591003e-02 > > 14 CCNF-Hs00171049_m1 I1 2.42086969 2.104210e-02 4.591003e-02 > > 3 ATR-Hs00169878_m1 J16 -2.32874362 2.407737e-02 5.024842e-02 > > 34 CDKN2D-Hs00176481_m1 J10 -2.19062609 3.304834e-02 6.609668e-02 > > 17 CCNK-Hs00395018_m1 J2 -2.18165397 3.542196e-02 6.801016e-02 > > 48 TP53BP2-Hs00610488_m1 I17 -1.92606707 6.038405e-02 1.114783e-01 > > 13 CCNE2-Hs00180319_m1 J18 1.85171704 7.355627e-02 1.307667e-01 > > 5 CCNA1-Hs00171105_m1 I22 1.68689949 9.901674e-02 1.697430e-01 > > 31 CDKN2A-Hs00233365_m1 J9 1.53778250 1.301844e-01 2.091751e-01 > > 40 MDM2-Hs00242813_m1 J14 -1.54259099 1.307344e-01 2.091751e-01 > > 21 CDC34-Hs00362082_m1 I9 -1.49644686 1.444121e-01 2.236059e-01 > > 26 CDK7-Hs00757090_g1 J8 -1.46834115 1.491629e-01 2.237444e-01 > > 37 E2F2-Hs00231667_m1 J12 -1.34939756 1.841182e-01 2.678083e-01 > > 1 18S-Hs99999901_s1 I11 -1.22892059 2.246587e-01 3.171652e-01 > > 11 CCND3-Hs00426901_m1 I15 1.19278926 2.393266e-01 3.282194e-01 > > 44 RBL1-Hs00765707_m1 J6 -1.09090637 2.849470e-01 3.799293e-01 > > 43 RB1-Hs00153108_m1 I24 0.94267649 3.498142e-01 4.538131e-01 > > 32 CDKN2B-Hs00793225_m1 I16 0.92879772 3.593685e-01 4.539392e-01 > > 42 PIN1-Hs00749260_s1 I7 0.82347162 4.139756e-01 5.095084e-01 > > 36 E2F1-Hs00153451_m1 J13 0.49857447 6.211263e-01 7.349228e-01 > > 22 CDK2-Hs00608082_m1 J7 0.48826165 6.277465e-01 7.349228e-01 > > 23 CDK4-Hs00364847_m1 I10 -0.31376143 7.554674e-01 8.614452e-01 > > 15 CCNG2-Hs00171119_m1 I21 0.29249852 7.717113e-01 8.614452e-01 > > 28 CDKN1A-Hs00355782_m1 J3 -0.25546174 7.999394e-01 8.634675e-01 > > 24 CDK5-Hs00358991_g1 J5 0.24250526 8.095008e-01 8.634675e-01 > > 38 EGFR-Hs00193306_m1 I6 -0.20599698 8.373903e-01 8.737986e-01 > > 8 CCNC-Hs00193177_m1 I8 -0.16344607 8.712155e-01 8.897520e-01 > > 20 CDC25C-Hs00156411_m1 I12 -0.06573621 9.479508e-01 9.479508e-01 > > ddCt FC meanCalibrator meanTarget categoryTarget > > 6 -1.07648601 2.1088932 28.95070 27.87422 Undetermined > > 35 -1.06811289 2.0966890 29.17518 28.10707 Undetermined > > 46 -1.49585130 2.8203052 28.35982 26.86397 Undetermined > > 4 1.58320841 0.3337389 28.55932 30.14253 Undetermined > > 47 0.76174256 0.5897835 27.28123 28.04298 OK > > 25 -0.49744752 1.4117137 27.19791 26.70046 Undetermined > > 33 1.12458260 0.4586347 29.01792 30.14251 Undetermined > > 16 0.49405366 0.7100273 27.59160 28.08565 OK > > 9 1.21875736 0.4296526 25.66984 26.88860 OK > > 18 -0.65334131 1.5728066 28.77853 28.12519 Undetermined > > 12 -0.90777004 1.8761433 30.28242 29.37465 Undetermined > > 29 0.75834453 0.5911743 25.70694 26.46529 OK > > 30 1.93646182 0.2612564 26.09796 28.03443 OK > > 45 0.48721017 0.7134033 27.09761 27.58482 OK > > 39 0.66461173 0.6308585 27.72870 28.39331 Undetermined > > 41 -0.96027455 1.9456801 28.29245 27.33217 Undetermined > > 7 -0.93770737 1.9154819 28.26303 27.32532 Undetermined > > 27 0.45887090 0.7275554 27.64381 28.10269 Undetermined > > 10 -0.45803273 1.3736674 26.74833 26.29030 OK > > 2 0.52684258 0.6940721 29.00257 29.52941 Undetermined > > 19 -0.92813803 1.9028186 27.69299 26.76485 Undetermined > > 14 NA NA NA 27.35398 Undetermined > > 3 0.35954577 0.7794099 28.23866 28.59821 Undetermined > > 34 0.36531112 0.7763014 28.26844 28.63375 OK > > 17 0.25381909 0.8386733 26.75291 27.00673 Undetermined > > 48 0.25068667 0.8404963 27.62105 27.87173 Undetermined > > 13 -0.41472318 1.3330429 30.47038 30.05566 Undetermined > > 5 NA NA NA NA Undetermined > > 31 -0.79234046 1.7318818 27.62496 26.83262 Undetermined > > 40 0.34543993 0.7870679 26.05771 26.40315 Undetermined > > 21 0.29287706 0.8162726 26.50089 26.79377 OK > > 26 0.22446161 0.8559144 27.93111 28.15557 Undetermined > > 37 0.50080229 0.7067137 28.44610 28.94690 Undetermined > > 1 1.04957648 0.4831100 9.89481 10.94439 OK > > 11 -0.22504377 1.1688127 26.96884 26.74380 Undetermined > > 44 0.29970271 0.8124198 28.77934 29.07904 Undetermined > > 43 -0.16428205 1.1206083 27.49565 27.33137 Undetermined > > 32 NA NA 28.34727 NA Undetermined > > 42 NA NA 25.12208 NA OK > > 36 -0.13237465 1.0960964 28.99034 28.85797 Undetermined > > 22 -0.08383105 1.0598287 29.05245 28.96862 Undetermined > > 23 0.13964048 0.9077453 25.07292 25.21256 OK > > 15 -0.05127164 1.0361778 27.77177 27.72050 Undetermined > > 28 0.15128081 0.9004507 22.74329 22.89457 OK > > 24 -0.04078961 1.0286767 28.16160 28.12081 Undetermined > > 38 0.04184529 0.9714117 26.29932 26.34117 Undetermined > > 8 0.02687468 0.9815443 27.06587 27.09275 OK > > 20 0.01922018 0.9867659 32.24171 32.26093 Undetermined > > categoryCalibrator > > 6 Undetermined > > 35 Undetermined > > 46 Undetermined > > 4 Undetermined > > 47 Undetermined > > 25 Undetermined > > 33 Undetermined > > 16 Undetermined > > 9 Undetermined > > 18 Undetermined > > 12 Undetermined > > 29 Undetermined > > 30 Undetermined > > 45 Undetermined > > 39 Undetermined > > 41 Undetermined > > 7 Undetermined > > 27 Undetermined > > 10 Undetermined > > 2 Undetermined > > 19 Undetermined > > 14 Undetermined > > 3 Undetermined > > 34 Undetermined > > 17 Undetermined > > 48 Undetermined > > 13 Undetermined > > 5 Undetermined > > 31 Undetermined > > 40 Undetermined > > 21 Undetermined > > 26 Undetermined > > 37 Undetermined > > 1 OK > > 11 Undetermined > > 44 Undetermined > > 43 Undetermined > > 32 Undetermined > > 42 OK > > 36 Undetermined > > 22 Undetermined > > 23 Undetermined > > 15 Undetermined > > 28 Undetermined > > 24 Undetermined > > 38 Undetermined > > 8 Undetermined > > 20 Undetermined > >> sessionInfo() > > R version 2.11.0 (2010-04-22) > > x86_64-pc-mingw32 > > > > locale: > > [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252 > > [3] LC_MONETARY=English_India.1252 LC_NUMERIC=C > > [5] LC_TIME=English_India.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] HTqPCR_1.2.0 limma_3.4.3 RColorBrewer_1.0-2 Biobase_2.8.0 > > > > > loaded via a namespace (and not attached): > > [1] affy_1.26.1 affyio_1.16.0 gdata_2.8.0 > > [4] gplots_2.8.0 gtools_2.6.2 preprocessCore_1.10.0 > >> > > > -- > Deepak Roshan V G > Laboratory Of Cell Cycle Regulation & Molecular Oncology > Division of Cancer Research > Regional Cancer Centre > Thiruvananthapuram > Kerala, India 695 011 >
cancer ddct cycle htqpcr assign • 667 views
ADD COMMENTlink written 8.1 years ago by Heidi Dvinge2.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 220 users visited in the last hour