Report builder feedback 18 nov 2011

Yang:

• Use but does not help you to 'get to know' the data in the first place.
• Wanted:
  • Quantative data: boxplot of measurements for each sample/individual, to inspect and detect/remove outliers -> Use e.g. boxplot(log(metaboliteexpression, exp(2.71828))) -> Or boxplot(log(t(metaboliteexpression), exp(2.71828))) for the (transposed) 'other view'
  • Qualitative data: heatmap like view of e.g. genotypes -> Use e.g. image(matrix(as.numeric(as.factor(genotypes)),nrow(genotypes),ncol(genotypes))) -> Or heatmap(matrix(as.numeric(as.factor(genotypes)),nrow(genotypes),ncol(genotypes)),scale="none",Colv=NA, Rowv=NA)

Basten:

• Enter gene -> get all eQTL information! Simple as can be.
• Cis/trans information
• Find genes in a region and get their QTLS (sounds like gBrowse)
• Ofcourse everything in document 'concept map'

Matthias:

• Need a bit more than just 'gene -> QTL' info, so like the Advanced button in the simple screen
• Select a matrix with QTL results, then grab a row or column (e.g. select a trait)
• Filter within that list using e.g. a threshold to get a smaller list of e.g. significant markers
• Using this trait and marker, build a nice table with a report
• Even more advanced: cross-datamatrix filtering. Select an individual and get from all matrices values which adhere to a certain filter.
• Relation between promotor-gene-transcript-protein-enzyme-pathways should be used preferably to create a biological valuable report
• gBrowse as an exploration tool would be super to have, and is reusable for many organisms

Panacea xQTL review Wed 9 nov 2011

• Data curation and annotation of the Panacea Database (joint effort)
• Host project analyses:
  • Phase 1: Just add the R scripts as files for basic provenance
  • Phase 2: Being able to rerun important scripts such as sample mislabeling and QTL x Env
  • Phase 3: Make it easy to add and run any R script that was used
• Data matrix:
  • Download or visualize with CytoScape
  • Need new view with more organization/hierarchy: group by experiment or annotation
  • Need to couple this hierarchy with the ability to quickly run scripts for visualization or statistics on a piece of the data
• Need 'supersearch' which produces reports on concepts (ie. everything related to a marker or individual)
  • This should include a special 'QTL finder' tool to quickly create reports on findings using a matrix and/or traits as inputs
• Focus on pathways:
  • Want to query pathway information for an organism from 1..N sources (GO, WormBase, KEGG.. ?)
  • Want to couple existing gene annotations to these pathways, semi-automatically (?)
  • Want to use this information to run analysis/visualizations on these batches of genes
  • Want to create pathway plots (biology!) with the gathered information (e.g. QTL profiles)
  • Want to create CytoScape graphs of e.g. correlation of the genes

EURATRANS xQTL review Wed 9 nov 2011

• Integrate with genome browser (gBrowse, formats WGL and GFF)
• Need to save any filter as a URL
• Need to clarify how a tool like gBrowse can specify a 'range' in filter URL syntax and link it
• Also need the 'range' to work on matrices with locus data (e.g. markers) via URL
• Need to add scripts as visualizers of data: e.g. let them appear in a list of possible plot types in matrix
• Search box bugs: no '_name' searches possible
• Use real column names instead of labels eventually, this is still very confusing
• Need for advanced matrix views:
  • On similar rows & columns, create 'subheaders' with multivalue display
  • Alternatively, matrix merge operation to concatenate them
  • Want to have a report on a value that appears in multiple matrices
  • And/or reports with plots for e.g. a marker or probe with all related information from all sources

xQTL LL user workshop Fri 28 Oct 2011 general comments

• Need more download formats: STATA, SAS, CSV (not TSV)
• SNP data should somehow include metadata such as: imputed (yes/no), genome build, reliability, dosage, etc.
• There should be a way to merge (part of a / a filtered) phenotype set with a genotype set, and retrieve the result
• The application can be slow, need more speed
• There are too many tabs, GUI is unclear
• Need an hourglass (or something) to indicate the application is busy (blackout screen with progress bar when busy, GeneNetwork style?)
• Making selections is too complex
• Column paging is confusing
• Filtering works 'half' (Joris please explain)
• Data viewer should be able to create selections using your own file
• Id's should be unrecognizable
• Search filter should work on all measurements by default
• Filters are lost when a user pages, this is annoying
• Like other waiting times, applying a filter should cause the app to refresh with a 'wait please' status
• Merging pheno- and geno sets is a special case of using a shopping cart (batches) to save selections for re-use elsewhere, this should be implemented. So you make a selection of participants based on phenotypic criteria, and then you view SNPs of interest for only those selected, and vice versa.