[BioC] Ringo: Error in preprocess() with R-2.7.0, but not with R-2.5.0
Ulrike Goebel
ugoebel at mpiz-koeln.mpg.de
Fri Jul 4 11:02:07 CEST 2008
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 at 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=en_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_IDENTIFICATION=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.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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