| | 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 | |
