Hello, we would like to analyze our time course data using maSigPro. The structure of edesign is following: > str(edesign.rna) int [1:16, 1:3] 30 30 30 30 45 45 45 45 60 60 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:16] "H030A_normalized_r1_ch1" "H030A_normalized_r2_ch1" "H030A_normalized_r3_ch1" "H030A_normalized_r4_ch1" ... ..$ : chr [1:3] "Time" "Replicate" "Hpy" The structure of data > str(data.rna) 'data.frame': 1280 obs. of 16 variables: $ H030A_normalized_r1_ch1: num 108.9 121.8 121.8 96 90.5 ... $ H030A_normalized_r2_ch1: num 131 127 138 117 129 ... $ H030A_normalized_r3_ch1: num 135 124 117 113 120 ... $ H030A_normalized_r4_ch1: num 109 105 107 101 103 ... $ H045A_normalized_r1_ch1: num 99.8 108.9 111.9 81.7 90.8 ... $ H045A_normalized_r2_ch1: num 102.9 99.2 108.5 104.8 82.3 ... $ H045A_normalized_r3_ch1: num 109.1 111 118.7 113 93.8 ... $ H045A_normalized_r4_ch1: num 69.1 82.6 79.6 91.6 76.6 ... $ H060A_normalized_r1_ch1: num 84.1 NA 91.5 113.7 84.1 ... $ H060A_normalized_r2_ch1: num 108.8 108.8 100 97.1 88.2 ... $ H060A_normalized_r3_ch1: num 95.3 79 98 92.6 70.8 ... $ H060A_normalized_r4_ch1: num 53.1 46.9 87.5 65.6 62.5 ... $ H075A_normalized_r1_ch1: num 96.4 112.5 112.5 96.4 112.5 ... $ H075A_normalized_r2_ch1: num 109.1 95.5 115.9 122.7 81.8 ... $ H075A_normalized_r3_ch1: num 91 91 112 123 91 ... $ H075A_normalized_r4_ch1: num 45.8 53.4 83.9 83.9 68.6 ... Using ts.analysis <- maSigPro(data.rna, edesign.rna) I got following output > ts.analysis <- maSigPro(data.rna, edesign.rna) [1] "running design" [1] "running p.vector" [1] "fitting gene 100 out of 1280" [1] "fitting gene 200 out of 1280" [1] "fitting gene 300 out of 1280" [1] "fitting gene 400 out of 1280" [1] "fitting gene 500 out of 1280" [1] "fitting gene 600 out of 1280" [1] "fitting gene 700 out of 1280" [1] "fitting gene 800 out of 1280" [1] "fitting gene 900 out of 1280" [1] "fitting gene 1000 out of 1280" [1] "fitting gene 1100 out of 1280" [1] "fitting gene 1200 out of 1280" [1] "running T.fit" [1] "fitting gene 100 out of 322" [1] "fitting gene 200 out of 322" [1] "fitting gene 300 out of 322" [1] "Warning: 76 genes with influential data at slot influ.info. Model validation for these genes is recommended" [1] "running get.siggenes" [1] "running see.genes 1" There were 50 or more warnings (use warnings() to see the first 50) and a Results.pdf -file in which the first time point is the mean of all time points ( mean(c(30,45,60,75))).. But I want to see each time point separately on the time-axis. What can be wrong ? > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] maSigPro_1.16.0 Biobase_2.4.1 loaded via a namespace (and not attached): [1] limma_2.18.0 Mfuzz_2.2.0 Regards Klaus-Peter -- Mit freundlichen Gr?ssen / Best regards Dr. Klaus-Peter Pleissner Max Planck Institute for Infection Biology Core Facility Bioinformatics Charit?platz 1 D-10117 Berlin Germany *Phone:* +49-30-28460-119 *Fax:* +49-30-28460-507 *URL:* http://web.mpiib-berlin.mpg.de/bioinformatik <http: web="" .mpiib-berlin.mpg.de="" bioinformatik=""/> *Email:* pleissner at mpiib-berlin.mpg.de <mailto:pleissner at="" mpiib-="" berlin.mpg.de="">