Problem with loading data into Piano

Question

[Parham]

Hi,

I am trying Piano package. In section 3.1 of vignette it creates a sample data and loads it. However I cannot reproduce it. It might be a very funny mistake or a bug but I checked every line several times. So no matter if I create the setup as object and load it or save it as a tab delimited and load it both ways it produces error. See codes below. Can anyone help with that please?

> mySetup
     oxygen      limitation
CAE1 "aerobic"   "Clim"
CAE2 "aerobic"   "Clim"
CAE3 "aerobic"   "Clim"
CAN1 "anaerobic" "Clim"
CAN2 "anaerobic" "Clim"
CAN3 "anaerobic" "Clim"
NAE1 "aerobic"   "Nlim"
NAE2 "aerobic"   "Nlim"
NAE3 "aerobic"   "Nlim"
NAN1 "anaerobic" "Nlim"
NAN2 "anaerobic" "Nlim"
NAN3 "anaerobic" "Nlim"
> library(piano)

> myArrayData <- loadMAdata(setup=mySetup)
Error in loadMAdata(setup = mySetup) :
  could not find any data files in directory

OR

> mySetup <- as.data.frame(mySetup)
> myArrayData <- loadMAdata(setup = mySetup)
Error in loadMAdata(setup = mySetup) :
  could not find any data files in directory

OR

> write.table(mySetup, file="setup.txt", sep="\t")
myArrayData <- loadMAdata()
Error in loadMAdata() : could not find any data files in directory

This is the list.files output:

list.files()
[1] "PJ022 - Piano.Rproj" "setup.txt"

Answer 1

[mirko.pavicic]

A bit late reply, but I was taking a look to the package and it seems the loadMdata function is expecting not only the setup file, but also CEL files or normalized data as put in the documentation

This function requires at least two inputs: (1) data, either CEL files in the directory specified by datadir or normalized data specified by dataNorm, and (2) experimental setup specified by setup.

I hope it helps other people since it has been almost seven years since this post.