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

[Ulrike Goebel]

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

-- 
  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