Re: [base] Dealing wiht duplicate spots

2011-11-22 Thread Nicklas Nordborg
On 2011-11-21 21:32, Nantel Andre wrote: We don't have any regular users yet since we are still figuring out how it works. I am doing everything from my administrator account. Have you created a file format configuration for the files you are using? This is done in Administrate - Plug-ins

Re: [base] Dealing wiht duplicate spots

2011-11-22 Thread Jari Häkkinen
On 2011-11-22 09.43, Nicklas Nordborg wrote: On 2011-11-21 21:32, Nantel Andre wrote: We don't have any regular users yet since we are still figuring out how it works. I am doing everything from my administrator account. Have you created a file format configuration for the files you are

Re: [base] Dealing wiht duplicate spots

2011-11-21 Thread Nicklas Nordborg
On 2011-11-21 17:08, Nantel Andre wrote: Greetings, We are currently trying to integrate BASE into our lab and writing the necessary plug-ins to import normalized data from ImaGene. Let's just say that the lack of documentation has been challenging. Right now we are trying to figure out how

Re: [base] Dealing wiht duplicate spots

2011-11-21 Thread Nicklas Nordborg
On 2011-11-21 19:23, Nantel Andre wrote: That issue goes beyond the ImaGene format. When doing contact printing of microarrays it is still fairly common to spot the same probe 2 or more times as shown in the example here (http://www.digitalapoptosis.com/2005/10/12/dna-microarray/). It is

Re: [base] Dealing wiht duplicate spots

2011-11-21 Thread Nantel Andre
On 2011-11-21, at 2:13 PM, Nicklas Nordborg wrote: The demo data set is a GenePix data set and for each spot the file contains the coordinates, reporter id and a lot of measured intensities and other values. So if your data is similar to this, then I think you don't need any special new

Re: [base] Dealing wiht duplicate spots

2011-11-21 Thread Nicklas Nordborg
On 2011-11-21 20:31, Nantel Andre wrote: On 2011-11-21, at 2:13 PM, Nicklas Nordborg wrote: The demo data set is a GenePix data set and for each spot the file contains the coordinates, reporter id and a lot of measured intensities and other values. So if your data is similar to this, then I

Re: [base] Dealing wiht duplicate spots

2011-11-21 Thread Nantel Andre
On 2011-11-21, at 2:51 PM, Nicklas Nordborg wrote: On 2011-11-21 20:31, Nantel Andre wrote: On 2011-11-21, at 2:13 PM, Nicklas Nordborg wrote: The demo data set is a GenePix data set and for each spot the file contains the coordinates, reporter id and a lot of measured intensities and