I have a batch of idat files that I would like to analyze using Immuminaio and lumi. This is the first time I have analyzed raw Illumina idat files and I have used neither Immuminaio nor lumi before. The problem I'll describe is not necessarily related to Illuminiao - it may be a problem with my idat files themselves.
If I read in the example data following the commands in the illuminaio.pdf vignette, the output data look correct, but when I read in one of my own idat files, the columns BackgroundBinData and BackgroundDevBinData have all values at '0'.
 657.5565 657.1952 657.0317 657.4821 657.4556 657.2791
 1.130837 1.345547 1.438468 1.250080 1.411696 1.081928
 0 0 0 0 0 0
 0 0 0 0 0 0
One of my idat files can be downloaded here: https://dl.dropboxusercontent.com/u/61432493/3998479036_A_Grn.idat
My questions are:
- Why are my idat files giving these 0 values? Has there been a problem during the data generation? (I no longer have access to any raw image data)
- Do I need these columns in order to proceed to downstream analyses in Lumi?
I have already tried running the batch through Lumi using some code given at Illumina Expression analysis from iDAT files, and I have encountered an issue there, but I don't know if this second issue is related to the problem I've just described. I can give more details if needed but, in brief: whereas the example.lumi batch that can be generated by following the lumi vignette contains the following element names: "beadNum, detection, exprs, se.exprs", but my own batch is missing the detection column - it contains only element names: "beadNum, exprs, se.exprs".
This seems to cause a problem when I try to do VST variance stabilizing transform. The following error is given:
> x.T <- lumiT(x)
Perform vst transformation ...
Error in !assayDataValidMembers(assayData(x.lumi), "detection") :
invalid argument type
Many thanks for any help.