Ringo: Error in preprocess() with R-2.7.0, but not with R-2.5.0
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Ulrike Goebel ▴ 110
@ulrike-goebel-2703
Last seen 10.2 years ago
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=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=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=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=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
probe annotate geneplotter affy vsn Ringo probe annotate geneplotter affy vsn Ringo • 1.4k views
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@joern-toedling-1244
Last seen 10.2 years ago
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=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=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=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=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 > > -- Joern Toedling EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Phone +44(0)1223 492566 Email toedling at ebi.ac.uk
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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
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Hello Ulrike, I agree that background correction does not make much sense here. "MM" probes, however, are an Affymetrix thing and I guess you mean that the red and green background estimates in the list elements Rb and Gb are all zero. I am going to remove the calling of "backgroundCorrect" within "preprocess" (currently happens for methods "loess" and "median" only) and leave it to the user if they want to call it separately on their RGList before calling "preprocess". In general, I did not find "loess" normalization very useful for two-color ChIP-chip data, since ChIP and input sample are usually very different from each other. So for the moment, I suggest you use another preprocessing method or, if you still want to use "loess", edit the function and remove the backgroundCorrect, or wait a few days for the new development version 1.5.6, which will include this change. Thanks for pointing out this potential problem. It's still funny that it worked with R2.5.0 but not with R2.7.0, though. Regards, Joern Ulrike Goebel wrote: > 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_ NAME=C;L >>> C_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFIC ATION=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 >>> >>> -- Joern Toedling EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Phone +44(0)1223 492566 Email toedling at ebi.ac.uk
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