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Hi,

Currently, processAssayXcmsSet() will obtain the first factor from the ISAtab
and use it as sampclass() for the xcmsSet. It would be great if all factors were used.
Below is an example.

Yours,
Steffen

# Create a data.frame with one column per factor
phenodataMtbls2 <- cbind(genotype=c("Col-0", "Col-0", "Col-0", "Col-0", "cyp79", "cyp79", "cyp79",  "cyp79", "Col-0", "Col-0", "Col-0", "Col-0", "cyp79", "cyp79",  "cyp79", "cyp79"), replicate=rep(c("Exp1", "Exp2"), each=8))

# add the assay names as rownames
rownames(phenodataMtbls2) <- c("MSpos-Ex1-Col0-48h-Ag-1_1-A,1_01_9818", "MSpos-Ex1-Col0-48h-Ag-2_1-A,1_01_9820",  "MSpos-Ex1-Col0-48h-Ag-3_1-A,1_01_9822", "MSpos-Ex1-Col0-48h-Ag-4_1-A,1_01_9824",  "MSpos-Ex1-cyp79-48h-Ag-1_1-B,1_01_9819", "MSpos-Ex1-cyp79-48h-Ag-2_1-B,2_01_9821",  "MSpos-Ex1-cyp79-48h-Ag-3_1-B,1_01_9823", "MSpos-Ex1-cyp79-48h-Ag-4_1-B,2_01_9825",  "MSpos-Ex2-Col0-48h-Ag-1_1-A,2_01_9827", "MSpos-Ex2-Col0-48h-Ag-2_1-A,3_01_9829",  "MSpos-Ex2-Col0-48h-Ag-3_1-A,4_01_9831", "MSpos-Ex2-Col0-48h-Ag-4_1-A,2_01_9833",  "MSpos-Ex2-cyp79-48h-Ag-1_1-B,3_01_9828", "MSpos-Ex2-cyp79-48h-Ag-2_1-B,4_01_9830",  "MSpos-Ex2-cyp79-48h-Ag-3_1-B,3_01_9832", "MSpos-Ex2-cyp79-48h-Ag-4_1-B,4_01_9834" )

# Assign to phenoData sloe in xcmsSet
phenoData(mtblsSet) <- phenodataMtbls2

# As you see, each assay file has its catenation of factors as sampclass().
sampclass(mtblsSet )
 [1] Col-0.Exp1 Col-0.Exp1 Col-0.Exp1 Col-0.Exp1 cyp79.Exp1 cyp79.Exp1
 [7] cyp79.Exp1 cyp79.Exp1 Col-0.Exp2 Col-0.Exp2 Col-0.Exp2 Col-0.Exp2
[13] cyp79.Exp2 cyp79.Exp2 cyp79.Exp2 cyp79.Exp2
Levels: Col-0.Exp1 cyp79.Exp1 Col-0.Exp2 cyp79.Exp2

otherwise some path error while creating xcmsSet

Dear all,
first of all many thanks for your nice work.
I'm currently working on an ISA tab file for a big Metabolights submission. The file was created with ISA creator with the 2014 Metabolights configuration file.
The file is composed of 1 investigation, 1 study and 7 different assays of different nature (i.e. I have 9 txt files in my folder). The automatic check of consistency of ISACreator is successful.
When I load the ISA tab file with Risa, however, I can find only 5 of my 7 assays. What can be the reason of that?
Thank you in advance for your help

Pietro

R: version 3.1.1 (2014-07-10)
Risa: Version: 1.8.0

Hi,

I got a bug report by mail. I have a patch, Pull request is imminent.
Yours,
Steffen

MTBLS37 has cdf files, could not find the investigation file? There is a "i_Investigation.txt" present in the folder
"…. if (!file.exists(file.path(path, ifilename))) stop("Did not find investigation file: ", :
the condition has length > 1 and only the first element will be used
Execution halted…"

I downloaded that for local debugging:

i <- readISAtab(".")
Error in file(file, "rt") : invalid 'description' argument
In addition: Warning message:
In if (!file.exists(file.path(path, ifilename))) stop("Did not find investigation file: ", :
the condition has length > 1 and only the first element will be used
traceback()
8: file(file, "rt")
7: read.table(file.path(path, ifilename), sep = "\t", fill = TRUE,
na.strings = "NA")
6: .local(.Object, ...)
5: initialize(value, ...)
4: initialize(value, ...)
3: new(Class = "ISATab", path = path)
2: readISAtabFiles(path, verbose)
1: readISAtab(".")

Browse[1]> path
[1] "."

Browse[1]> ifilename
[1] "a_creinhardtii_metabolite profiling_mass spectrometry.txt"
[2] "i_Investigation.txt"
[3] "m_creinhardtii_metabolite profiling_mass spectrometry_v2_maf.tsv"

just needs moving around from inst/doc

Hi,

readISAtab() fails for http://www.ebi.ac.uk/metabolights/publicfiles/MTBLS25

with an

Error in validObject(.Object) :
invalid class "ISAtab" object: invalid object for slot "assay.filenames.per.sample" in class "ISAtab": got class "NULL", should be or extend class "character"

I think Risa should fail gracefully on this.

Steffen

P.S.: The ISAtab files are also available from
https://github.com/nmrML/nmrML/tree/master/examples/SteffensMTBL_MetaboquantConverterExamples/mtbls25

oerc-dynamic-226:R-packages agbeltran$ R CMD INSTALL Risatab

• installing to library ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
• installing source package ‘Risatab’ ...
  ** R
  ** inst
  ** preparing package for lazy loading
  Warning: Class "C++Object" is defined (with package slot ‘Rcpp’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘.GlobalEnv’
  ** help
  *** installing help indices
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded
  *** arch - i386
  During startup - Warning message:
  Class "C++Object" is defined (with package slot ‘Rcpp’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘.GlobalEnv’
  *** arch - x86_64
  During startup - Warning message:
  Class "C++Object" is defined (with package slot ‘Rcpp’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘.GlobalEnv’
• DONE (Risatab)

The base.url provided in the getExpressionSet example is no longer accessible. The example, therefore, can not be executed.

I have no other way to assess this function and check it's expected output.

Extend the code to work with all possible ISATab patterns

http://bioconductor.org/checkResults/2.12/bioc-LATEST/Risa/george2-buildsrc.html
http://bioconductor.org/checkResults/2.13/bioc-LATEST/Risa/zin1-buildsrc.html

with

** testing if installed package can be loaded
Error in namespaceExport(ns, exports) :
undefined exports: getRawDataFilenames, getAssayRawDataFilenames, getMicroarrayAssayFilenames, isMicroarrayAssay, getMIAMEMetadata, getExpressionSet

If my ISA directory contains editor backup files like "i_Investigation~"
then I get:

ISAmtbls <- readISAtab()

Error in file(file, "rt") : invalid 'description' argument
In addition: Warning message:
In if (!file.exists(file.path(path, ifilename))) stop("Did not find investigation file: ",  :
  the condition has length > 1 and only the first element will be used

I will check if this line https://github.com/ISA-tools/Risa/blob/master/R/AllGenerics.R#L122
needs to grep with line ending like ^ ... $ .
Yours,
Steffen

Hi,

BioC is reporting a WARNING:
http://www.bioconductor.org/packages/devel/bioc/html/Risa.html
Yours, Steffen

* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'AssayTab,ANY,ANY,ANY'
  generic '[' and siglist 'ISATab,ANY,ANY,ANY'
  generic '[<-' and siglist 'AssayTab,ANY,ANY,ANY'
  generic '[<-' and siglist 'ISATab,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.