Hello Dr. Du,

Thank you so much for your quick reply.

One of the files provided to me by our core facility did include  
BEAD_STDERR (as well as the other columns you mentioned), and I got  
this error when I attempted to load that file:

 > probe_file <- lumiR("Probe.txt", lib = "lumiRatV1")
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

After receiving this error, the set "probe_file" is not created. When  
I take a look at Probe.txt using Excel, it's immediately clear that  
the ARRAY_STDEV column for each array has "NaN" in each cell. In the  
experimentation, I removed these columns to see what if any effect it  
had on my attempts to read the file; I received an identical error  
message to the one above when I attempted to import data lacking  
ARRAY_STDEV columns.

Session info is the same as was provided in the previous email. Thank  
you so much for your assistance with this, it's greatly appreciated!



On Jul 31, 2008, at 3:11 PM, Pan Du wrote:

> Hi Alison,
>
> I guess the data you have does not include the “BEAD_STDERR”  
> columns, which are required to create LumiBatch object. lumiR will  
> create an ExpressionSet object if the “BEAD_STDERR” columns are not  
> available in the file.
>
> Ask your core facility to output “AVG_Signal”, “BEAD_STDERR”,  
> “Detection Pval” columns, probably also “Avg_NBEADS”. If there are  
> not many samples, I recommend output all columns BeadStudio can  
> output.
>
>
> Pan
>
>


Alison Ziesel
Department of Ophthalmology, Emory University
aziesel@emory.edu




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