Latest updates Updates
2000-06 Older dChip
versions
8/9/07: Bug corrected: an error when reading reference normal or combined genotype file existed in dchip versions from 6/29/07 to 8/8/07. It affected these functions: LOH analysis (LD-HMM and haplotype correction); Reading external genotype call file for CEL files without paired genotype call file (e.g. SNP 5.0 and 6.0 data). (Discussion)
8/4/07: Can analyze SNP 6.0 arrays (SNPs but not CNV probes). Use this genome info file. (Discussion)
7/22/07: Can specify a "RefBatch" column in sample information to indicate batches for copy number analysis.
6/29/07: Can analyze SNP 5.0 arrays (SNPs but not CNV probes). Use this genome info file. (Discussion)
4/16/07: Chromosome regions may be specified when analyzing SNP data. When reference genes are specified as chromosome regions, it may be helpful to focus attention on the copy number/LOH events in these genes.
4/4/07: At the gene clustering view, if a gene cluster is selected, "Tools/Gene function enrichment" can analyze this cluster of genes. The function term names in summary table are also sorted.
3/31/07: The function terms of redundant probe sets for the same genes will only be counted once at gene function enrichment analysis ("Tools/Gene Function Enrichment" and gene clustering) and when reading gene information file at "Open group", whether "Tools/Options/Mask redundant probe set" is checked or not. A summary table of enrichment analysis is output in the analysis view.
3/24/07: When making gene information file, gene symbols will be added in the gene name column of gene information file. (Discussion)
2/28/07: If the probe set mask file has "Including" in the first line, the file will be regarded as a probe set inclusion file and only the probe sets in this file will be included in the cdf.bin file and downstream analysis.
2/26/07: At "Analysis/Compare samples/Combine comparison",
check "Make M-A plot"
to plot log ratio against log product of the two groups' mean expression level.
2/1/07: (1) At "Open group", specify "Suffix of TXT/CHP file" as ".chp" to read expression or SNP calls from CHP files. This avoids converting CHP files to TXT files to use in dChip.
(2) At the chromosome view, toggle "Chromosome/Draw Average Curve" to show single-sample or average LOH or copy number data across samples.
1/23/07: Select the menu "Chromosome/Draw All Curves" at the chromosome view to show the data curves of all samples.
1/4/07: At “Chromosome/Clustering”, checking “Export sample ordering into ‘sample_order.txt’” will export a text file into the working directory after clustering. This file contains sample names as ordered by clustering.
(Updated 12/6/07)