[BioC] Ringo: Error in preprocess() with R-2.7.0, but not with R-2.5.0

[Joern Toedling]

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_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.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
>
>   

-- 
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