I just found you are using lumi 1.4.0. Please use the latest released
version lumi 1.6.2 or developing version, and use R 2.7 or later. There are
many updates after 1.4.0.
Also please send me the top 10 lines of your data file, you do not need to
cc to bioconductor mailing list.  Thanks!

Pan


On 7/31/08 2:50 PM, "Alison Ziesel" <aziesel@emory.edu> wrote:

> 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 ³BEAD_STDERR² columns, which
>> are required to create LumiBatch object. lumiR will create an ExpressionSet
>> object if the ³BEAD_STDERR² columns are not available in the file.
>>  
>>  Ask your core facility to output ³AVG_Signal², ³BEAD_STDERR², ³Detection
>> Pval² columns, probably also ³Avg_NBEADS². 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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