xps package - import.expr.scheme help
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@jordansquair-12276
Last seen 5.0 years ago

Hello,

I am trying to process some expression data using the xps package and having some trouble importing the root schemes for the probes. Here is the code: 

`library(xps)

## define paths
scmdir <- paste(path.package("xps"), "/schemes", sep = "")
libdir <- "mypath//libraryfiles"
anndir <- "mypath/Annotation"

# Process root scheme for A-AFFY-18
A.AFFY.18 <- import.expr.scheme("A_AFFY_18", filedir=scmdir,
                                           schemefile=file.path(libdir, "RG_U34A.cdf"),
                                           probefile=file.path(libdir, "A-AFFY-18.probe.tab"),
                                           annotfile=file.path(anndir, "A-AFFY-18.annot.csv"))'

Resulting in: 

Error: Could not create file </Library/Frameworks/R.framework/Versions/3.3/Resources/library/xps/schemes/A_AFFY_18.root>
Error in import.expr.scheme("A_AFFY_18", filedir = scmdir, schemefile = file.path(libdir,  : 
  error in function ‘ImportExprSchemes’

sessioninfo: 

R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.2

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] rat2302.db_3.2.3     org.Rn.eg.db_3.4.0   mouse4302.db_3.2.3   org.Mm.eg.db_3.4.0   AnnotationDbi_1.36.2
 [6] IRanges_2.8.1        S4Vectors_0.12.1     limma_3.30.9         affy_1.52.0          Biobase_2.34.0      
[11] BiocGenerics_0.20.0  xps_1.34.0          

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9           digest_0.6.12         DBI_0.5-1             RSQLite_1.1-2        
 [5] BiocInstaller_1.24.0  zlibbioc_1.20.0       affyio_1.44.0         preprocessCore_1.36.0
 [9] tools_3.3.2           memoise_1.0.0        

 

Probeset data derived from:

https://www.ebi.ac.uk/arrayexpress/files/A-AFFY-18/?ref=E-GEOD-464

 

Appreciate any help.

xps root R affy • 951 views
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cstrato ★ 3.9k
@cstrato-908
Last seen 3.3 years ago
Austria

Hello,

To create expression 'schemes' package 'xps' uses the original cdf, probe and annotation 
files from Affymetrix, which all contain the name of the array, in your case 'RG_U34A'.

Method 'import.expr.scheme()' is expecting files containing the name of the array.
See the examples 'xps/examples/script4schemes.R' how to do this for array 'RG_U34A'

Regards,
Christian

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@jordansquair-12276
Last seen 5.0 years ago

Hi Christian,

Thanks for the quick reply. I have pulled the necessary files from Affymetrix and followed your example, 

`scheme.rgu34a.na31 <- import.expr.scheme("rgu34a",filedir=file.path(scmdir, "na31"),
                                         schemefile = file.path(libdir,"RG_U34A.cdf"),
                                         probefile  = file.path(libdir,"RG_U34A.probe.tab"),
                                         annotfile  = file.path(anndir,"RG_U34A.na31.annot.csv"))`

However, I am still getting this:

Error: Could not create file </Library/Frameworks/R.framework/Versions/3.3/Resources/library/xps/schemes/rgu34a.root>
Error in import.expr.scheme("rgu34a", filedir = file.path(scmdir), schemefile = file.path(libdir,  : 
  error in function ‘ImportExprSchemes’

Appreciate your help.

 

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Entering edit mode
cstrato ★ 3.9k
@cstrato-908
Last seen 3.3 years ago
Austria

Hi,

First, please note that my examples in 'script4schemes.R' are only examples. You need to adapt
them to your needs:
- RG_U34A.na31.annot.csv is very old, you should download the newest version
- did you create the directories before using 'file.path(scmdir, "na31")'?

Second, I consider it a bad idea to use 'paste(path.package("xps"), "/schemes", sep = "")' as 
'scmdir', especially on the Mac. You should never store things in '/Library/Frameworks/...'!
I am not even sure whether you have write permissions to the '/Library' directory on the Mac,
so this may be your mistake.

Please create a directory in your home directory to store data, e.g. use something like:
/Users/jordansquair/MyWorkspace/ if your username is 'jordansquair'

If you still get error messages please set parameter 'verbose=TRUE' in method 'import.expr.scheme()',
and run R from 'xterm'. Please send me the complete output.

Regards,
Christian

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@jordansquair-12276
Last seen 5.0 years ago

Hi Christian,

Thanks for you help with this. I've re-located the directories and still seem to be getting the same error message. I've set verbose=TRUE and run in xterm. Here is the output:

diffexpr/Preprocess-DiffExpr-xps.R
Loading required package: methods
Error: cannot open file "iostream"  /var/tmp/tmp.4.Uch9s4_cint:2:
*** Interpreter error recovered ***

Welcome to xps version 1.34.0
    an R wrapper for XPS - eXpression Profiling System
    (c) Copyright 2001-2015 by Christian Stratowa
    
Error: Could not create file </Users/jordansquair/MyWorkspace/schemes/na36/rgu36a.root>
Error in import.expr.scheme("rgu36a", filedir = file.path(scmdir, "na36"),  : 
  error in function 'ImportExprSchemes'
Execution halted

Thanks.

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Entering edit mode
cstrato ★ 3.9k
@cstrato-908
Last seen 3.3 years ago
Austria

Hi, 

The first error indicates an installation problem:
- How did you install ROOT?
- Did you set ROOTSYS and other variables as indicated in README?
- Which version of ROOT are you using? 

Please tell me the exact name of the ROOT file that you have downloaded.

Regards,
Christian

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