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(/s/tetex-1.0/share/texmf/tex/latex/ae/t1aess.fd File: t1aess.fd 1997/11/16 Font definitions for T1/aess. ) Overfull \vbox (21.68121pt too high) has occurred while \output is active [] [1 Non-PDF special ignored! Non-PDF special ignored! [/s/tetex-1.0/share/texmf/dvips/config/pdftex.map]] Overfull \vbox (21.68121pt too high) has occurred while \output is active [] [2] Overfull \hbox (2.37668pt too wide) in paragraph at lines 206--206 []\T1/aer/bx/n/17.28 The Gamma Gamma and Log-nor-mal Nor-mal mod- [] Overfull \vbox (21.68121pt too high) has occurred while \output is active [] [3] Overfull \vbox (21.68121pt too high) has occurred while \output is active [] [4] Overfull \hbox (24.49081pt too wide) in paragraph at lines 279--293 [][] [] LaTeX Warning: Reference `eq:cll' on page 5 undefined on input line 300. Overfull \vbox (21.68121pt too high) has occurred while \output is active [] [5] LaTeX Font Info: Font shape `T1/aess/m/it' in size <12> not available (Font) Font shape `T1/aess/m/sl' tried instead on input line 366. Overfull \vbox (21.68121pt too high) has occurred while \output is active [] [6] Overfull \vbox (21.68121pt too high) has occurred while \output is active [] [7] Overfull \vbox (21.68121pt too high) has occurred while \output is active [] [8] Overfull \vbox (21.68121pt too high) has occurred while \output is active [] [9] Overfull \vbox (21.68121pt too high) has occurred while \output is active [] [10] ! You can't use `macro parameter character #' in vertical mode. l.482 # gg.em.out <- emfit(exprdata, family = "GG", Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! You can't use `macro parameter character #' in horizontal mode. l.483 # patterns, verbose = TRUE, num.iter = 50, Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! You can't use `macro parameter character #' in horizontal mode. l.484 # theta.init = c(7, 1, 1), p.init = c(0.95, 0.05)) Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! You can't use `macro parameter character #' in vertical mode. l.486 # gg.post.out<-postprob(gg.em.out,exprdata) Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! You can't use `macro parameter character #' in vertical mode. l.488 # sum(gg.post.out[,2]>0.5) Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! You can't use `macro parameter character #' in vertical mode. l.490 # lnn.em.out <- emfit(exprdata, family = "LNN", patterns, verbose = TRU Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! You can't use `macro parameter character #' in horizontal mode. l.491 # num.iter=50,theta.init = c(7, 1, 1), p.init = c(0.95, 0.05)) Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. Overfull \hbox (29.11903pt too wide) in paragraph at lines 490--492 []\T1/aess/m/n/12 lnn.em.out <- em-fit(exprdata, fam-ily = "LNN", pat-terns, ve r-bose = TRU num.iter=50,theta.init [] ! You can't use `macro parameter character #' in vertical mode. l.494 # lnn.post.out<-postprob(lnn.em.out,exprdata) Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! You can't use `macro parameter character #' in vertical mode. l.496 # sum(lnn.post.out[,2]>0.5) Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! You can't use `macro parameter character #' in horizontal mode. l.497 # sum(gg.post.out[,2]>0.5&lnn.post.out[,2]>0.5) Sorry, but I'm not programmed to handle this case; I'll just pretend that you didn't ask for it. If you're in the wrong mode, you might be able to return to the right one by typing `I}' or `I$' or `I\par'. ! Misplaced alignment tab character &. l.497 # sum(gg.post.out[,2]>0.5& lnn.post.out[,2]>0.5) I can't figure out why you would want to use a tab mark here. If you just want an ampersand, the remedy is simple: Just type `I\&' now. But if some right brace up above has ended a previous alignment prematurely, you're probably due for more error messages, and you might try typing `S' now just to see what is salvageable. Overfull \vbox (21.68121pt too high) has occurred while \output is active [] [11] Overfull \vbox (21.68121pt too high) has occurred while \output is active [] [12] Overfull \vbox (21.68121pt too high) has occurred while \output is active [] [13] Overfull \hbox (390.7679pt too wide) in paragraph at lines 619--619 []\T1/aett/m/n/12 gg4group.em.out<-emfit(exprdata,family="GG",patterns4group,ve rbose=T,num.iter=50,theta.init=c(7,1,1),p.init=c(0.90, 0.05, 0.025, 0.025))[] [] Overfull \vbox (21.68121pt too high) has occurred while \output is active [] [14] Overfull \hbox (403.1038pt too wide) in paragraph at lines 619--619 []\T1/aett/m/n/12 lnn4group.em.out<-emfit(exprdata,family="LNN",patterns4group, verbose=T,num.iter=50,theta.init=c(7,1,1),p.init=c(0.90, 0.05, 0.025, 0.025))[] [] Overfull \hbox (8.35478pt too wide) in paragraph at lines 644--644 []\T1/aett/m/n/12 > gene.ids<-(1:1000)[gg4group.post.out[,2]>0.5&lnn4group.post .out[,2]>0.5][] [] Overfull \vbox (21.68121pt too high) has occurred while \output is active [] [15] Overfull \vbox (21.68121pt too high) has occurred while \output is active [] [16] (vignette.aux) LaTeX Warning: There were undefined references. ) Here is how much of TeX's memory you used: 4542 strings out of 10631 55726 string characters out of 193306 119245 words of memory out of 1052001 7434 multiletter control sequences out of 10000+0 35124 words of font info for 77 fonts, out of 400000 for 1000 14 hyphenation exceptions out of 1000 35i,8n,36p,328b,312s stack positions out of 300i,100n,500p,50000b,10000s Output written on vignette.pdf (16 pages, 163459 bytes).