Paper
1. M. Dai; P. Wang; E. Jakupovic; S. J. Watson; F. Meng (2007) Web-Based GeneChip Analysis System for Large-Scale Collaborative Projects. Bioinformatics 2007; doi:10.1093/bioinformatics/btm297
2. M. Dai, P. Wang, A.D. Boyd, G. Kostov, B. Athey, E. G. Jones, W. E. Bunney, R. M. Myers, T. P. Speed, H. Akil, S. J. Watson, F. Meng (2005) Evolving Gene/Transcript Definitions Significantly Alter the Interpretation of GeneChip Data. Nucleic Acid Research 33 (20), e175
Demos
WGAS interface introduction
Set up a new analysis
Modify an existing analysis job
Retrieve analysis results
Common features of all WGAS pages
How to use wizard of the Script page
How to install our python package MBNIUM
How to upload your own celfiles to WGAS
How to upload your own gene level data for FunctionScore analysis
How to mine analysis result
To upload data, click MBNIUM Python package
To analyze data, click Web-based GeneChip Analysis System and use to sign-on if you haven't an account here. Or sign-up at here
Cel files in GEO
A job scheduler downloads Cel files from NCBI GEO ftp site every night. And every week it would also check if Cel files are re-uploaded by owner. If owner modified the Cel file, it would be re-downloaded.
Cel files selection
1. In page 'Start', select Task 'Create a new analysis' and the DataGroup you want to analyze, and click icon 'Next'
2. In page 'Criteria', select an option from the dropdown list 'Column', Then the list 'Value' would be refreshed. Click any option in the list 'Value' and then click the button 'Append to Criteria'. A string would be appened to the text box 'Criteria'. And the list 'Value' would be refreshed again. And then change list 'Column' to make further filter, or click icon 'Next' to select individual files. Please note multiple selection in the list 'Value' can be made by holding Control key.
3. In page 'celfiles', click the check box to select celfile that would be analyzed, or click the top check box to select the whole list. Clicking the column would sort the file list. When selection is done click icon 'Next' to continue.
Define sample grouping
One must define at least one factor here if he would need "Probe Set Level Analysis" or "Gene Set Level Analysis" in page 'Anaylysis'.
In page 'Factor', select a column from dropdown list 'Select', the column name would be in the text box 'Edit'. Then click button "Add as factor", the factor values and their group would appear, Those group could be modified by user. The factor could be removed by clicking it. Please note that the string can be edited by adding SQL functions. For example, substr(TITLE, 7, 3) would get the 7th, 8th, 9th character from column TITLE.
After factors are defined, click icon 'Next' to continue.
Select Cdf File
In dropdown list 'Custom CDF' of page 'Analysis', select a custom CDF for your analysis, or select 'None' for original cdf.
Select ProbeFilter
In dropdown list 'Probe Filter' of page 'Analysis', select a kind of probe filter.
Splicing
In dropdownlist 'Probe Level Analysis' of page 'Analysis', select option 'splicing_rma' or 'splicing_rma_snpprobefilter'. 'splicing_rma' would do rma analysis with both the latest ENSG and ENSE custom CDF, then splicing the analysis result. 'splicing_rma_snpprobefilter' would do the same, plus it would remove all allele-specific probes.
Probe Level analysis
In dropdownlist 'Probe Level Analysis' of page 'Analysis', select any analysis other than 'splicing_rma'.
Probe Set Level analysis
In dropdownlist 'Probe Set Level Analysis' of page 'Analysis', select one anaylysis. The analysis would use result of 'Probe Level Analysis' as input.
Gene Set Level analysis
In dropdownlist 'Gene Set Level Analysis' of page 'Analysis', select one anaylysis. The analysis would use result of 'Probe Level Analysis' as input.
Other Analysis
In dropdownlist 'Other Analysis' of page 'Analysis', select one anaylysis. The analysis would use the function ReadAffy's result as input