1. This is a depression research in a F2 intercross of rat strain F344 and WKY. The data set had been used in 7 publications for different phenotypes. The cross file posted in website is merged form 3 separated files related with these papers;


2. We can't update the map since we only have B37 Cox map and MGI database for mouse. So we still use the original genetic map in the new merged data file and the file is saved as "Solberg2004_F344xWKY_Data.csv". This file is ready to be read into Rqtl;


3. Generate a description file of the project, it includes the general information, paper information, definitions of phenotypes and the description of alleles;


4. For the genotypes of the cross:
(1) Keep the genetic map as same as the original file in the new data file;

(2) Remove the extra spaces in genotype part in new file;

(3) Correct a typo in one marker on chr 6 (change "D8Rat128"->"D6Rat128");

(4) There are 5 alleles in the genotypes: a=F344, b=WKY, c=not WKY, d=not F344 and h=heterozygote;

(5) A "c" allele on X chromosome is detected and omitted by Rqtl program after data input, it is set as missing automatically in R. Moreover, the program uses fuction jittermap() to adjust the markers which are at same positions.


5. For the phenotypes of the cross:
(1) The new cross file is merged from 3 separated cross files, it includes all the phenotypes used in 7 papers listed in the description file;

(2) Remove trait "adrenalwkwgt" from new cross file (suggested by Gary in 11/1/2010);

(3) The definition of the trait "litter"and the intervention of the rats are not found in the papers (they were highlighted with blue color). 


6. Except the "csv" data file mentioned above, I saved the description file and merged data file with original map together as a big excel file ("Data_Description_FxW_Solberg2004.xlsx"). (first curation is finished on 7/10/2009, all the files are updated on 9/15, 11/1/2010)