Changes between Version 7 and Version 8 of xQTLBiologistImport

Timestamp:

2011-09-08T09:41:14+02:00 (13 years ago)

Author:

jvelde

Comment:

--

xQTLBiologistImport

@@ -12 +12 @@
 Please note:
 * The filename is used as data matrix name. Choose it carefully.
-* The created matrices are tagged as Rqtl analysis pheno or geno datasets. They will appear when running a default QTL analysis.
-* Marker and chromosome annotations are automatically created in the database because they are needed for QTL analysis.
+* The created data matrices are tagged as Rqtl analysis pheno or geno datasets. They will appear when running a default QTL analysis.
+* When uploading a map file, marker and chromosome annotations are created in the database.
 * Individual and trait (phenotype) annotations are not automatically created.
+* It is good practice to also annotate your individuals and traits. In fact, for certain analysis types this is required. (Genetical Genomics, trait heritability estimation, etc)
+* Different seperators are recognized in all file uploads. Usual ones include tab, whitespace or comma.
+
+=== Help: my QTL analysis fails! ===
+
+Please check the following:
+* The markers in the genotype matrix must be annotated in the map file. The names must exactly match. Check use the ''Inspector'' tool in ''View data'' to verify data consistency. You can always manually add or manipulate markers at any point using ''View annotations'', click ''Markers''.
+* For a correct new data set, the exact same individual names must be used in the genotype and phenotype file.
 * The QTL analysis needs to know which type of cross was used. It looks at the annotation of the '''first individual''' of the genotypes to get cross type from the ''ontologyReference'' field. Set this to e.g. ''xgap_rqtl_straintype_riself'' to indicate the cross is a recombinant inbred line by selfing. The coding is taken from Rqtl.