Function updates

Download the latest dChip here (64 bit version).
 

4/4/10: To export all CEL images automatically, at the CEL image view, select "View/Export Image", check "Export to file" and "Export all images individually".

4/4/10: Cluster SNP samples using major copy proportion data.

3/19/10: At "View/Online database", specify a UCSC genome assembly number such as "hg19" or "mm9" to select the corresponding assembly.

2/28/10: Specify organism as "mouse" at "Analysis/Chromosome" for mouse SNP arrays. Can handle original unsorted cytoband files.
 
2/21/10: "Tools/Make information file" handles the latest Gene Ontology files.
 

1/9/09: Added gene information files for Gene ST arrays and the Python code to make them.

 

6/20/08: (1) Use “Tools/Automate” to automate dChip analysis functions.

(2) In SNP copy number analysis, check “Options/Chromosome/Infer MCP” to infer major copy proportions.

 

3/24/08: You can use "Open group/Get External data" to update a sample info file while in a session, instead of reading all data again. Check "Update" after "Sample info" in this dialog. (suggested by Charles Mullighan)

 

2/17/08: At “Analysis/Chromosome/Options”, specify a “Chromosome result file” and select “Write” or “Read” to store inferred LOH or copy numbers in a binary data file during an initial session, and read these data back in later sessions.

 

2/12/08: SNP 6.0 and SNP 5.0 genome info files now include one for the CNV probes. The two files may be combined in a text editor to view SNP and CNV probes together. The AFFY-SNP- probe sets will also be included in the CDF.BIN file if you check “ignore existing dcp and cdf.bin file” to re-extract data.

 

2/4/08: “Chromosome/Linkage analysis”: The “vector sum is 0” error is handled when “Apply inheritance vector reduction” is checked, so that sporadic LOD score peaks are eliminated and result in smoother LOD curve. “Options/Score/Use one of every X markers” can be set to have a quicker analysis using a subset of markers. If “out of memory” error occurs, reducing “Options/Chromosome/HMM length” will help.