Hi, I am postdoc working with genome wide gene expression using Poplar oligonucleotide Nimblgen array. I am beginner in R and bioconductor. I have Nimblgen raw data in .pair file format. I dont know how to use that using Oligo vignette which is available in bioconductor. How to have input file in R format from .pair files? Thanks Dhriaj -- Dhiraj Naik Postdoctoral Research Associate [[alternative HTML version deleted]]

Dhiraj Naik wrote: > Hi, > I am postdoc working with genome wide gene expression using Poplar > oligonucleotide Nimblgen array. I am beginner in R and bioconductor. I have > Nimblgen raw data in .pair file format. I dont know how to use that using > Oligo vignette which is available in bioconductor. How to have input file in > R format from .pair files? > Thanks > Dhriaj The oligo package loads .xys files, not .pair files. If you did the hybridizations in your own lab, use NimbleScan to generate .xys files from the tiff images. If you got your data from the service lab, contact technical support and ask them to generate the .xys files for your order. Todd