[BioC] error using lumiR * correction

[Kristen Dang]

Kristen K Dang <kristen.dang at ...> writes:

> I am trying to use the lumiR function from the lumi package to read in a
BeadStudio output file, but I keep
> getting the following error:
> 
> > input_file = "sample_probe_profile.txt";
> > data = lumiR(input_file, lib = 'lumiHumanV1')
> Error in mget(targetID, get(paste(lib, "TARGETID2NUID", sep = ""), mode =
"environment"),  : 
>   invalid first argument
> In addition: Warning message:
> In formatC(as.numeric(id), width = width, flag = "0", format = "d") :
>   NAs introduced by coercion
...

On further investigation, I find that it is not the lumiR function itself that
is causing the errors. I can run lumiR like so with the following error messages:

data = lumiR(input_file)
Warning message:
In addNuId2lumi(x.lumi, lib = lib) :
  Please provide the annotation file or lumi annotation library!

The earlier error (below) comes when I do this:
data = addNuId2lumi(data, lib = 'lumiHumanV1')
Error in mget(targetID, get(paste(lib, "TARGETID2NUID", sep = ""), mode =
"environment"),  : 
  invalid first argument
In addition: Warning message:
In formatC(as.numeric(id), width = width, flag = "0", format = "d") :
  NAs introduced by coercion

I get a similar error, and a new one, when I do the following:
addControlData2lumi("control_probe_profile.txt", data)
[1] "Inputting the data ..."
[1] "Adding nuID to the data ..."
Error in data.frame(controlType = controlType, ProbeID = ProbeID, controlData) : 
  arguments imply differing number of rows: 0, 784
In addition: Warning message:
In addNuId2lumi(x.lumi, lib = lib) :
  Please provide the annotation file or lumi annotation library!


So my questions that remain:
What is the problem with the addNuID function?
What am I doing wrong regarding use of the control information?

If anyone has insight about the use of lumi, please let me know! I would be very
grateful.