sorry, I forgot to CC to the list .. ---------- Forwarded Message ---------- Subject: Re: [BioC] Ringo: Error in preprocess() with R-2.7.0, but not with R-2.5.0 Date: Friday 04 July 2008 11:00 From: Ulrike Goebel <ugoebel@mpiz-koeln.mpg.de> To: Joern Toedling <toedling at="" ebi.ac.uk=""> Hi Joern, thanks for your suggestion .. but this didn't help: I'm still getting the same error. Trying to trace it back, I found that it is generated in backgroundCorrect debug: res <- .Internal(optim(par, fn1, gr1, method, con, lower, upper)) Stack trace: where 1: optim(par = c(mu, log(sigma), log(alpha)), fn = normexp.m2loglik.saddle, control = list(trace = as.integer(trace)), x = x) where 2: switch(method, saddle = optim(par = c(mu, log(sigma), log(alpha)), fn = normexp.m2loglik.saddle, control = list(trace = as.integer(trace)), x = x), neldermean = optim(par = c(mu, log(sigma), log(alpha)), fn = normexp.m2loglik, control = list(trace = as.integer(trace)), x = x), bfgs = optim(par = c(mu, log(sigma), log(alpha)), fn = normexp.m2loglik, gr = normexp.grad, method = c("BFGS"), control = list(trace = as.integer(trace)), x = x)) where 3: normexp.fit(x, method = method) where 4: backgroundCorrect(RG$G - RG$Gb, method = method, verbose = verbose) where 5: switch(method, subtract = { [lines omitted] where 6: backgroundCorrect(myRG, method = "normexp", offset = 50) where 7: preprocess(test2[test2$genes$Status == "Probe", ], method = "loess", returnMAList = TRUE, bc.method = "none") I realize that preprocess is using backgroundCorrect(myRG, method = "normexp", offset = 50), without a way to change the correction method. Actually, in my datasets (and generally in NimbleGen data ?), the MM probes are not used, and the corresponding column is all-zero. So why at all would one want to apply a background correction method ? What I still don't understand is that the problem is happening only with this one array (I can't see anything special with it) ... Greetings & thanks for the quick answer ! Ulrike On Thursday 03 July 2008 18:16, you wrote: > Hi Ulrike, > I cannot be sure but I guess the problem is related these warnings in > 2.5.0, which indicated that there was already something amiss back then. > > > Warning messages: > > 1: NaNs produced in: log(x) > > 2: NaNs produced in: log(x) > > Which probes produce the NaN values? It could be the "Random" ones. > Unless there is a good reason, why you want to keep these control probes > that do not match the genome in your data for further analyses, I would > suggest to drop them before preprocessing. > > loess_test <- preprocess(test[test$genes$Status=="Probe",], > method="loess",returnMAList=TRUE) > > > If you want to keep the Random probes, maybe you should discard only > those that have missing values already in the RGList. > Hope this helps. > > Regards, > Joern > > Ulrike Goebel wrote: > > Dear list, > > > > I find that I cannot normalize one (of several) NimbleGen files in > > R-2.7.0 (using the preprocess() function of package Ringo), while I did > > normalize this dataset successfully before with R-2.5.0. I guess this is > > not even a problem of Ringo, but rather of normalizeWithinArrays (and > > thus of limma), or ? > > > > Here is what I get with R.2.7.0 (and also with R.6.0, not shown): > >> test <- readNimblegen("TFL2HA.txt", "spottypes.txt", path=dir[[2]]) > > > > Reading targets file... > > Reading raw intensities... > > Read header information > > Read 127612_532.pair > > Read 127612_635.pair > > Read 1276122_532.pair > > Read 1276122_635.pair > > Determining probe categories... > > Matching patterns for: GENE_EXPR_OPTION PROBE_ID > > Found 385991 Probe > > Found 0 Negative > > Found 0 H_Code > > Found 0 V_Code > > Found 3316 Random > > Setting attributes: values Color > > > >> loess_test <- preprocess(test, method="loess",returnMAList=TRUE ) > > > > Background correction... > > Green channel > > Corrected array 1 > > Error in if (all(abs(delta) < 1e-10)) break : > > missing value where TRUE/FALSE needed > > > >> sessionInfo() > > > > R version 2.7.0 (2008-04-22) > > x86_64-unknown-linux-gnu > > > > locale: > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UT > >F-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;L > >C_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICA TION=C > > > > attached base packages: > > [1] splines tools stats graphics grDevices utils datasets > > [8] methods base > > > > other attached packages: > > [1] Ringo_1.4.0 SparseM_0.77 RColorBrewer_1.0-2 > > [4] vsn_3.6.0 affy_1.18.0 preprocessCore_1.2.0 > > [7] affyio_1.8.0 limma_2.14.1 geneplotter_1.18.0 > > [10] annotate_1.18.0 xtable_1.5-2 AnnotationDbi_1.2.0 > > [13] RSQLite_0.6-8 DBI_0.2-4 lattice_0.17-6 > > [16] genefilter_1.20.0 survival_2.34-1 Biobase_2.1.7 > > > > loaded via a namespace (and not attached): > > [1] grid_2.7.0 KernSmooth_2.22-22 > > > > > > ------------------------------------------------------------------ ------- > >---------------------------------- .. and this is with R.2.5.0 > > > >> test <- readNimblegen("TFL2HA.txt", "spottypes.txt", path=dir[[2]]) > > > > Reading targets file... > > Reading raw intensities... > > Read header information > > Read 127612_532.pair > > Read 127612_635.pair > > Read 1276122_532.pair > > Read 1276122_635.pair > > Determining probe categories... > > Matching patterns for: GENE_EXPR_OPTION PROBE_ID > > Found 385991 Probe > > Found 0 Negative > > Found 0 H_Code > > Found 0 V_Code > > Found 3316 Random > > Setting attributes: values Color > > > >> loess_test <- preprocess(test, method="loess",returnMAList=TRUE ) > > > > Background correction... > > Corrected array 1 > > Corrected array 2 > > Normalizing... > > Warning messages: > > 1: NaNs produced in: log(x) > > 2: NaNs produced in: log(x) > > > >> sessionInfo() > > > > R version 2.5.0 (2007-04-23) > > x86_64-unknown-linux-gnu > > > > locale: > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UT > >F-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;L > >C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ IDENTIF > >ICATION=C > > > > attached base packages: > > [1] "tools" "stats" "graphics" "grDevices" "utils" > > "datasets" [7] "methods" "base" > > > > other attached packages: > > Ringo RColorBrewer vsn affy affyio > > limma "1.0.0" "1.0-2" "2.2.0" "1.14.2" "1.4.1" > > "2.10.5" geneplotter lattice annotate Biobase > > "1.14.0" "0.15-4" "1.14.1" "1.14.1" > > > > > > Best, Ulrike -- Dr. Ulrike Goebel Bioinformatics Support Max-Planck Institute for Plant Breeding Research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062 121 ------------------------------------------------------- -- Dr. Ulrike Goebel Bioinformatics Support Max-Planck Institute for Plant Breeding Research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062 121