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Question: xps package - import.expr.scheme help
0
gravatar for jordansquair
9 months ago by
jordansquair0 wrote:

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.

ADD COMMENTlink modified 9 months ago by cstrato3.8k • written 9 months ago by jordansquair0
0
gravatar for cstrato
9 months ago by
cstrato3.8k
Austria
cstrato3.8k wrote:

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

ADD COMMENTlink written 9 months ago by cstrato3.8k
0
gravatar for jordansquair
9 months ago by
jordansquair0 wrote:

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.

 

ADD COMMENTlink written 9 months ago by jordansquair0
0
gravatar for cstrato
9 months ago by
cstrato3.8k
Austria
cstrato3.8k wrote:

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

ADD COMMENTlink written 9 months ago by cstrato3.8k
0
gravatar for jordansquair
9 months ago by
jordansquair0 wrote:

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.

ADD COMMENTlink written 9 months ago by jordansquair0
0
gravatar for cstrato
9 months ago by
cstrato3.8k
Austria
cstrato3.8k wrote:

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

ADD COMMENTlink written 9 months ago by cstrato3.8k
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