| 1 | == Notes Morris xQTL workbench review meeting 4 march 2011 @ GBIC == |
| 2 | Attending: Yang, Maria, Frank, Danny, Joeri, Morris |
| 3 | |
| 4 | Priorities: |
| 5 | (1) Loading data foramts, universal data loading functions |
| 6 | (2) Mislabeling scripts [need 'news' place where this can be viewed'] |
| 7 | (3) Pathway picture + QTL + linkout + gene expression + phenotypes |
| 8 | |
| 9 | Frank: |
| 10 | * Storing your data |
| 11 | * Running quick analyses |
| 12 | * Quality control of the data (standard, missing markers) |
| 13 | * Every new collaboration data sets are different slightly; standardized solution |
| 14 | * Time investing of matrix cleaing (missing data, wrong columns); have these times of parsing |
| 15 | * Pulldown button for format parsers; inventory of how these data sets look like |
| 16 | * Set based select all the trans regulated probes |
| 17 | |
| 18 | Maria: |
| 19 | * Starting to learn R |
| 20 | * Having a button for standard analyses |
| 21 | * Preliminary analysis tool |
| 22 | * Prefer to look at the code |
| 23 | |
| 24 | Yang: |
| 25 | * To do analyses and run it in parallel myself |
| 26 | * Can test my code on the machine and get error message (requirement) |
| 27 | * Expected gains: have more R tools on this, for pictures, tables |
| 28 | * Expected gains: |
| 29 | * Standard importers for Agilent, Affymetrix, Nimblegen |
| 30 | * Do you show all annotation of a particular gene, which gene it is, located, is there a SNP |
| 31 | * Can we make a pathway picture; I want to submit all my genes there and I know the relations. See QTL and Pathway plots together, possibly in different conditions or factors. |
| 32 | |
| 33 | Danny: |
| 34 | * What additional you want (boxploting, histograms, common jobs) |
| 35 | * Would the data formats you use |
| 36 | |
| 37 | Joeri: |
| 38 | * Want to have pathway |
| 39 | |
| 40 | Name candidate: |
| 41 | Omics workbench. |
| 42 | |
| 43 | |