Hi All,

I am trying to read an idat file from an Illumina genotyping array that uses VeraCode microbeads technology. This is my code and the error I get:

> library(illuminaio)
> idat <- readIDAT("E:/Ck01EC032-VBP_R001_C001_GRN.idat")
Error in idx[i, 1] : subscript out of bounds

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] IlluminaDataTestFiles_1.3.1 illuminaio_0.8.0           

loaded via a namespace (and not attached):
[1] base64_1.1  tools_3.1.2

Any help is greatly appreciated.

Thank you,

Laura

Thank you for the fast reply, Kasper.

I will be happy to share the file with you. What is the most convenient way to share it?

Laura

Dropbox it is: https://www.dropbox.com/s/wsls0eb0hkovi3n/Ck01EC032-VBP_R001_C001_GRN.idat?dl=0

Thank you, Kasper!

Laura

________

Laura Acion, PhD

University of Iowa, USA

National Scientific and Technical Research Council, Argentina

lacion@gmail.com

Hi Laura,

If you check out version 0.9.1 from the Biconductor devel branch illuminaio should now be able to read the file you uploaded.  I've never worked with VeraCode data, so I'm not sure what to expect the output to look like, but there's a lot of 0s and not many intensities.  Perhaps that's what you're expecting, but if it isn't please contact me and we'll work on making sure illuminaio is reading the data correctly.

Thanks,

Mike

Hi Mike,

Thanks a lot for looking into this. I was able to open our files using the new version of illuminaio. It seems the file I sent you was problematic and that is why you were getting a lot of 0s. A different file yields:

> head(idat$Quants)
  MeanBinData TrimmedMeanBinData DevBinData MedianBinData BackgroundBinData
1   11774.799         11884.2500  1000.1562    12031.4170                 0
2    5392.514          5422.7046   242.7697     5300.4170                 0
3    2880.954          2891.2720   116.9060     2865.5835                 0
4     135.381           140.1218    63.5149      123.0833                 0
5    3670.702          3690.5874   225.5330     3688.9167                 0
6    3231.911          3263.2666   225.6001     3187.0833                 0
  BackgroundDevBinData CodesBinData NumBeadsBinData NumGoodBeadsBinData
1                    0           10              17                  17
2                    0           23              12                  12
3                    0           33              20                  20
4                    0           44              14                  14
5                    0           51              21                  21
6                    0           54              16                  16

We are new to VeraCode data too, but this is more reassuring than all 0s :-)

Thanks a lot for your help.

Best wishes,

Laura

Hi Kasper and Mike,

If you decide to add a VeraCode file to IlluminaTestDataFiles you can find the one I included in my previous post here: https://www.dropbox.com/s/vhaah8gu2k7p3sz/TestPlaca1R004_C005_RED.idat?dl=0

Thanks again for fixing this so fast.

Best wishes,

Laura