[BioC] xps: hugene11 chip gives problems

cstrato cstrato at aon.at
Thu Jan 10 21:10:29 CET 2013 

Dear Philip,

I have just tried a subset of CEL-files from the Affymetrix 
"gene_1_1_st_ap_tissue_sample_data" for HuGene_1.1 array, but I cannot 
repeat the error you get. Here is my output for one CEL-file only:

 > library(xps)

Welcome to xps version 1.19.1
     an R wrapper for XPS - eXpression Profiling System
     (c) Copyright 2001-2013 by Christian Stratowa

 > scheme <- root.scheme("./na33/hugene11stv1.root")
 > x.xps <- import.data(scheme, "tmp_x", celdir = "./cel", celfiles = 
"HumanBrain_1.CEL", verbose = TRUE)
Opening file <./na33/hugene11stv1.root> in <READ> mode...
Creating new temporary file 
</Volumes/MitziData/CRAN/Workspaces/hugene11/tmp_x_cel.root>...
Importing <./cel/HumanBrain_1.CEL> as <HumanBrain_1.cel>...
    hybridization statistics:
       1 cells with minimal intensity 17.5
       1 cells with maximal intensity 22402.1
New dataset <DataSet> is added to Content...
 > cat("The loaded .CEL-files are:\n");
The loaded .CEL-files are:
 > for (i in 1:length(rawCELName(x.xps, fullpath = FALSE)))
+   cat(sprintf("%s\n", rawCELName(x.xps, fullpath = FALSE)[i]));
HumanBrain_1.CEL
 >
 > sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] xps_1.19.1

loaded via a namespace (and not attached):
[1] tools_2.15.0
 >


As you see everything is ok. I did also run the triplicates of the Brain 
and Prostate samples and could do RMA w/o problems.

Could you please try the following two options:

1, Could you try to use the CEL-files from the Affymetrix dataset to 
make sure that there is no problem with the CEL-files.

2, I see that you did create the ROOT scheme files in directory:
scmdir <- paste(.path.package("xps"), "schemes/", sep = "/")

I must admit that I have never tried to store the scheme files in the 
package directory, since I have the feeling that this may cause 
troubles, especially when you update R and/or the xps package to a new 
version.
Could you please try to save your file "hugene11stv1.root" in a 
different directory such as '/home/degroot/schemes' or better to create 
this file in this directory, and then try if you still get the problem.

Best regards,
Christian


On 1/10/13 1:03 PM, Groot, Philip de wrote:
> Hi Christian,
>
> I am trying to do an analysis using xps and the hugene11 chip. However,
> I run into problems for which I need your help.
>
> I created a small test-script to demonstrate the problem:
>
> library(xps)
>
> scheme <-
> root.scheme("/local2/R-2.15.2/library/xps/schemes/hugene11stv1.root")
>
> x.xps <- import.data(scheme, "tmp_x", celdir = ".", celfiles =
> "G092_A05_01_1.1.CEL", verbose = TRUE)
>
> cat("The loaded .CEL-files are:\n");
>
> for (i in 1:length(rawCELName(x.xps, fullpath = FALSE)))
>
>    cat(sprintf("%s\n", rawCELName(x.xps, fullpath = FALSE)[i]));
>
> Upon execution, I get:
>
>> library(xps)
>
> Welcome to xps version 1.18.1
>
>      an R wrapper for XPS - eXpression Profiling System
>
>      (c) Copyright 2001-2012 by Christian Stratowa
>
>> scheme <- root.scheme("/local2/R-2.15.2/library/xps/schemes/hugene11stv1.root")
>
>> x.xps <- import.data(scheme, "tmp_x", celdir = ".", celfiles = "G092_A05_01_1.1.CEL", verbose = TRUE)
>
> Opening file </local2/R-2.15.2/library/xps/schemes/hugene11stv1.root> in
> <READ> mode...
>
> Creating new temporary file
> </mnt/geninf16/home/guests/pdegroot/dataanalysis/PHILIPG/tmp_x_cel.root>...
>
> Importing <./G092_A05_01_1.1.CEL> as <G092_A05_01_1.1.cel>...
>
>     hybridization statistics:
>
>        1 cells with minimal intensity 19
>
>        1 cells with maximal intensity 21364.4
>
> New dataset <DataSet> is added to Content...
>
>>
>
>> cat("The loaded .CEL-files are:\n");
>
> The loaded .CEL-files are:
>
>> for (i in 1:length(rawCELName(x.xps, fullpath = FALSE)))
>
> +   cat(sprintf("%s\n", rawCELName(x.xps, fullpath = FALSE)[i]));
>
> Error: Tree set <> could not be found in file content
>
> Error: Tree set <> could not be found in file content
>
> NA
>
> The weird thing is: I only have this problem with the hugene11 chip. As
> far as I can see, al other chips work properly (still na32 based).
>
> This effects all other steps, because there is no “content” to normalise
> etc.
>
> I created the root-scheme as follows:
>
> scmdir <- paste(.path.package("xps"), "schemes/", sep = "/")
>
> scheme <- import.exon.scheme("hugene11stv1",filedir=scmdir,
> layoutfile=paste(libdir, "HuGene-1_1-st-v1.r4.clf", sep="/"),
> schemefile=paste(libdir,"HuGene-1_1-st-v1.r4.pgf", sep="/"),
> probeset=paste(anndir,"HuGene-1_1-st-v1.na33.1.hg19.probeset.csv",
> sep="/"),
> transcript=paste(anndir,"HuGene-1_1-st-v1.na33.1.hg19.transcript.csv",
> sep="/"), add.mask = TRUE)
>
> (libdir and anndir are also defined off course).
>
> I even updated the na32 annotation to the latest Affymetrix version
> (na33) the exclude a problem there. It does not fix the issue.
>
> Please note that I am running root version 5.32/04 as version 5.32/01 is
> no longer available for download. Root works properly as far as I can see.
>
> Do you have any clue where this problem originates from? Thank you!
>
> sessionInfo():
>
>> sessionInfo()
>
> R version 2.15.2 (2012-10-26)
>
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>
>   [7] LC_PAPER=C                 LC_NAME=C
>
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>
> [1] xps_1.18.1
>
> loaded via a namespace (and not attached):
>
> [1] tools_2.15.2
>
> Regards,
>
> *Dr. Philip de Groot
> Bioinformatician / Microarray analysis expert*
>
> Wageningen University / TIFN
> Netherlands Nutrigenomics Center (NNC)
>
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> PO Box 8129, 6700 EV Wageningen
> Visiting Address:
>
> "De Valk" ("Erfelijkheidsleer"),
>
> Building 304,
> Verbindingsweg 4, 6703 HC Wageningen
> Room: 0052a
> T: 0317 485786
> F: 0317 483342
> E-mail: Philip.deGroot at wur.nl <mailto:Philip.deGroot at wur.nl>
> I: http://humannutrition.wur.nl <http://humannutrition.wur.nl/>
>
> https://madmax.bioinformatics.nl
>
> http://www.nutrigenomicsconsortium.nl
> <http://www.nutrigenomicsconsortium.nl/>
>
> 	
>

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