Question

error in import.exon.scheme, XPS package

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Biologist ▴ 120

@biologist-9801

Last seen 4.7 years ago

Dear Christian,

I am new to XPS and following your paper on using XPS for my Gene St array (HuGene-2_0-st design). I need the degradation plot.

I used the listed code to create scheme object:

> scmdir <- "D:/GeneST_Analyse/CELFiles/schemes"
> libdir <- "D:/GeneST_Analyse/CELFiles/libraryfiles"
> anndir <- "D:/GeneST_Analyse/CELFiles/Annotation"
> scheme.hugene20stv1.na35 <- import.exon.scheme("Scheme_HuGene20stv1_na35",filedir=scmdir,layoutfile=paste(libdir,"HuGene-2_0-st.clf",sep="/"),schemefile=paste(libdir,"HuGene-2_0-st.pgf",sep="/"),probeset=paste(anndir,"HuGene-2_0-st-v1.na35.hg19.probeset.csv",sep="/"),transcript=paste(anndir,"HuGene-2_0-st-v1.na35.hg19.transcript.csv",sep="/"))

I got the following error. Could you please give me any suggestion?

Error Message:

Error in import.exon.scheme("Scheme_HuGene20stv1_na35", filedir = scmdir, :
error in function ‘ImportExonSchemes’

Thanks in Advance

xps import.exon.scheme error rnadegradationplot • 1.6k views

ADD COMMENT • link 8.8 years ago • updated 8.7 years ago Biologist ▴ 120

score 0 · Answer 1 · 2016-02-26

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cstrato ★ 3.9k

@cstrato-908

Last seen 6.1 years ago

Austria

Dear Venkatesh,

Could you please answer the following questions:
- sessionInfo()
- which version of Windows do you use?
- how do you run R?

Please try the following to run on the Windows Console, i.e. RTerm with 'verbose=TRUE',
and send me the complete output from the Console:

scheme.hugene20stv1.na35 <- import.exon.scheme("Scheme_HuGene20stv1_na35",filedir=scmdir,
layoutfile=file.path(libdir,"HuGene-2_0-st.clf"),
schemefile=file.path(libdir,"HuGene-2_0-st.pgf"),
probeset=file.path(anndir,"HuGene-2_0-st-v1.na35.hg19.probeset.csv"),
transcript=file.path(anndir,"HuGene-2_0-st-v1.na35.hg19.transcript.csv"),
verbose=TRUE)

Note: On Windows you will see the verbose messages only when starting R from the command line,
i.e. using RTerm.

Regards,
Christian

ADD COMMENT • link 8.8 years ago cstrato ★ 3.9k

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Hi Christian,

Thanks for the reply. I tried running on windows console i.e. RTerm.

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] xps_1.30.0

loaded via a namespace (and not attached):
[1] tools_3.2.3

Output:

R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]

> library('xps')

Welcome to xps version 1.30.0
an R wrapper for XPS - eXpression Profiling System
(c) Copyright 2001-2015 by Christian Stratowa

> scmdir <- "D:/GeneST_Analyse/CELFiles/schemes"
> libdir <- "D:/GeneST_Analyse/CELFiles/libraryfiles"
> anndir <- "D:/GeneST_Analyse/CELFiles/Annotation"
> scheme.hugene20stv1.na35 <- import.exon.scheme("Scheme_HuGene20stv1_na35",fi$
+ layoutfile=file.path(libdir,"HuGene-2_0-st.clf"),
+ schemefile=file.path(libdir,"HuGene-2_0-st.pgf"),
+ probeset=file.path(anndir,"HuGene-2_0-st-v1.na35$
+ transcript=file.path(anndir,"HuGene-2_0-st-v1.na$
+ verbose=TRUE)
SysError in <TFile::TFile>: file D:/GeneST_Analyse/CELFiles/schemes/Scheme_HuGen
e20stv1_na35.root can not be opened (No such file or directory)
Error: Could not create file <D:/GeneST_Analyse/CELFiles/schemes/Scheme_HuGene20
stv1_na35.root>
Error in import.exon.scheme("Scheme_HuGene20stv1_na35", filedir = scmdir, :
error in function 'ImportExonSchemes'

Please help me out. Thank you !!

ADD REPLY • link 8.7 years ago Biologist ▴ 120

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HI Christian,

It worked now. Thank you !

ADD REPLY • link 8.7 years ago Biologist ▴ 120

score 0 · Answer 2 · 2016-03-01

Hi Christian,

For RNA degradation plot I am getting an error. Please check the following:

load existing ROOT scheme file and ROOT data file

scheme.exon <- root.scheme(paste(scmdir,"Scheme_HuGene20stv1_na35.root",sep="/"))
data.exon <- root.data(scheme.exon, paste("D:/GeneST_Analyse/CELFiles/rootdata/tmp_data_exon_cel.root",sep="/"))

qualification - rlm

rlm.all <- rmaPLM(data.exon, "tmp_exonRLMall", filedir=getwd(), tmpdir="", qualopt="all", option="transcript", exonlevel="affx+core", add.data=FALSE)

(or)

rlm.all <- fitRLM(data.exon,"tmp_exonRLM", qualopt="all", option="transcript", exonlevel="affx+core", verbose=FALSE)

And I get the following error:

Creating new temporary file <D:/GeneST_Analyse/CELFiles/tmp_exonRLMall.root>...
Opening file <D:/GeneST_Analyse/CELFiles/schemes/Scheme_HuGene20stv1_na35.root>
in <READ> mode...
Opening file <D:/GeneST_Analyse/CELFiles/rootdata/tmp_data_exon_cel.root> in <RE
AD> mode...
Preprocessing data using method <preprocess>...
Calculating quality control for <raw> data trees ...
setting selector mask for typepm <9276>
setting selector mask for typepm <9276>
calculating quality controls for <44796> of <51991> units...Finished.
calculating border elements for <X_8__HuGene_2_0_st__raw.brd>...
center of intensity:
positive border elements (x,y) = <0.301687, 0.0508869>.
negative border elements (x,y) = <-0.228422, -0.0683751>.
calculating border elements for <E__HuGene_2_0_st__raw.brd>...
center of intensity:
positive border elements (x,y) = <0.0752159, 0.194383>.
negative border elements (x,y) = <-0.159563, -0.0453415>.
calculating border elements for <GG7__HuGene_2_0_st__raw.brd>...
center of intensity:
positive border elements (x,y) = <0.481647, -0.0256652>.
negative border elements (x,y) = <-0.196879, -0.0731834>.
calculating border elements for <J__HuGene_2_0_st__raw.brd>...
center of intensity:
positive border elements (x,y) = <0.112615, 0.00776396>.
negative border elements (x,y) = <-0.1127, -0.0283493>.
calculating border elements for <O__HuGene_2_0_st__raw.brd>...
center of intensity:
positive border elements (x,y) = <0.119527, 0.141888>.
negative border elements (x,y) = <-0.124044, -0.0194095>.
calculating border elements for <T__HuGene_2_0_st__raw.brd>...
center of intensity:
positive border elements (x,y) = <0.219297, -0.114559>.
negative border elements (x,y) = <-0.144787, 0.0191627>.
Background correcting raw data...
calculating background for <X_8__HuGene_2_0_st_.cel>...
Error: Number of PMs or MMs is zero.
An error has occured: Need to abort current process.
Error in .local(object, ...) : error in rwrapper function 'Preprocess'

Please help me out. Thank you !