1. The map in original data file had been updated to Build37 Cox genetic map (in cM) by authors already, save the file as "Hageman2011_MRLxSM_B37_Data.csv". This file is ready to be read into Rqtl; 


2. Generate a description file of the project, it includes the general information, definitions of the phenotypes and description of the genotypes;


3. For the genotypes of this cross: (cM=centimorgan, bp=basepair)
(1) Change the symbol of MRL allele from "MM" to "M" and SM allele from "SS" to "S" (standard format in data sets of QTL archive) and save the changes in B37 data file; 

(2) The markers and the genetic map was updated by author already, the information is complete and no more problems are detected in genotypes;


4. For the phenotypes of the cross:
(1) This is an eQTL project and the phenotypes are composed with 8 traditional traits and 33,871 gene expression data. The expression data was generated by Affymetrix GeneChips (Mouse Gene 1.0 ST) and it had been cleaned by the authors already;

(2) EXCEL cannot load the file completely if it has huge amount of columns. We transposed the columns and rows and save the changes in B37 data. The data file can be opened by EXCEL or other softwares. If users use Rqtl to do data analysis, the format of the file should be set as "csvr" (CSV reversed file); 

(3) Unlike traditional traits, there is no description for gene expression data. The names of the data are ensembl transcript ids -- the identifier for the transcripts;

(4) This cross only has 173 male mice in total and it is a one direction cross; 


5. Except the "csv" file mentioned above, I also saved the description file and data process together as a big excel file ("Data_Description_MRLxSM_Hageman2011.xlsx"). For eQTL projects, the size of original data and B37 data file is very large and they are not added in excel file anymore. (1st curating work is finished on 6/2/2011).


6. Information updated on 10/25/2011: 
(1) Change the B37 Cox map from Male Centimorgans to Sex-Average Centimorgans in B37 data file and description file (information are updated on 10/25/2011); 

(2) Quality control plots (genetic map, missing genotypes plot, map comparision plot and whole genome RF plot) performed and no issues found. All quality control plots were saved in ÒQCReport_Hageman2011.pdfÓ.