I am having a spot of trouble with file conversion. I am trying to test for multiple correction using SNPSpD (http://gump.qimr.edu.au/general/daleN/SNPSpD/). I have my files in a normal plink ped and map format.
The ped file has 6 columns, and then the alleles. I've opened the ped file in excel, removed the sixth column, and then saved it as a pre file.
For the map file, the plink format has 4 columns. The merlin format has 3 columns. In the plink format, I've changed the first column to make it the marker id, left the second column as it is and then added pseudo marker-positions in the 3rd column and deleted the fourth column.
I tried loading it in SNPSpD, but it doesn't seem to like my file and isn't giving me any results. Does anyone know what is going on and what I am doing wrong?