[BioC] xps error

[cstrato]

Dear Juan,

I have never seen this warning message, but my current version of R is 
still R-2.15.0. Maybe, the R-developers have decided to issue a warning 
message in R-2.15.1, since I am using the C++ code "cout" for my messages.

I am forwarding this to BioC so maybe someone can comment on this issue. 
Especially, why it says: "partial output only".

However, you can definitely ignore this warning message, but is the 
output indeed only partial?

Best regards,
Christian


On 10/2/12 10:47 PM, Juan Fernandez Tajes wrote:
> Dear Christian,
>
> I´m trying to use xps for analyzing HuGene 1.1 st array from Affymetrix,
> I´ve used the following code for creating the root scheme:
>
> libdir<- "/Users/juane/Investigación/INIBIC/Affymetrix Raw Data/Analisis
> xps/libraryfiles"
> anndir<- "/Volumes/GigaDrive/Affy/Annotation"
> scmdir<- "/Users/juane/Investigación/INIBIC/Affymetrix Raw Data/Analisis
> xps/schemes"
>
> scheme.hugene11stv1.na32 <- import.exon.scheme("hugene11stv1", filedir =
> file.path(scmdir, "na32"),
>                              file.path(libdir,
> "HuGene-1_1-st-v1_strip_libraryfile", "HuGene-1_1-st-v1.r4.clf"),
>                              file.path(libdir,
> "HuGene-1_1-st-v1_strip_libraryfile", "HuGene-1_1-st-v1.r4.pgf"),
>                              file.path(anndir, "Version08Oct",
> "HuGene-1_1-st-v1.na32.hg19.probeset.csv"),
>                              file.path(anndir, "Version08Oct",
> "HuGene-1_1-st-v1.na32.hg19.transcript.csv"))
>
> However when I execute the following code for importing the data, I got
> a warning:
>
> data.test <- import.data(scheme.hugene11st, "tmpdt_data.test",
> celdir=celdir, celfiles=celfiles, verbose=T)
> Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw
> Data/CEL/10SE208.CEL> as <X10SE208.cel>...
>     hybridization statistics:
>        1 cells with minimal intensity 11.5
>        1 cells with maximal intensity 22789.9
> Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw
> Data/CEL/10SE209.CEL> as <X10SE209.cel>...
>     hybridization statistics:
>        5 cells with minimal intensity 12.3
>        1 cells with maximal intensity 22839.2
> Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw
> Data/CEL/10SE210.CEL> as <X10SE210.cel>...
>     hybridization statistics:
>        1 cells with minimal intensity 11.5
>        1 cells with maximal intensity 20892.7
> Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw
> Data/CEL/10SE211.CEL> as <X10SE211.cel>...
>     hybridization statistics:
>        1 cells with minimal intensity 10.5
>        1 cells with maximal intensity 22303.1
> Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw
> Data/CEL/10SE212.CEL> as <X10SE212.cel>...
>     hybridization statistics:
>        2 cells with minimal intensity 11.5
>        1 cells with maximal intensity 20283.4
> Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw
> Data/CEL/10SE213.CEL> as <X10SE213.cel>...
>     hybridization statistics:
>        1 cells with minimal intensity 8.3
>        1 cells with maximal intensity 21714.6
> Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw
> Data/CEL/10SE214.CEL> as <X10SE214.cel>...
>     hybridization statistics:
>        2 cells with minimal intensity 12
>        1 cells with maximal intensity 21296.2
> Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw
> Data/CEL/10SE215.CEL> as <X10SE215.cel>...
>     hybridization statistics:
>        2 cells with minimal intensity 11.8
>        1 cells with maximal intensity 19225.4
> Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw
> Data/CEL/10SE216.CEL> as <X10SE216.cel>...
>     hybridization statistics:
>        2 cells with minimal intensity 11.5
>        1 cells with maximal intensity 21394.9
> Importing </Users/juane/Investigación/INIBIC/Affymetrix Raw
> Data/CEL/10SE218.CEL> as <X10SE218.cel>...
>     hybridization statistics:
>        1 cells with mini
> (WARNING: partial output only, ask package author to use Rprintf instead!)
> mal intensity 12.8
>        1 cells with maximal intensity 21774.8
>
> I think when I build the root.scheme for HuGene 1.1 st I got a similar
> warning,
>
> Is this warning an important issue?
>
> Many thanks
>
> Juan
>
>