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Software |
dChip Software: Analysis and visualization of
gene expression and SNP microarrays
dChip software Introduction Manual References Tutorials Download User Forum Yahoo Group Past Updates dChip course from Bioinformatics.org (5/19-23) Search manual & site Developed by Cheng Li Lab and Wing Wong Lab. Supported by National Institutes of Health, Belfer
Foundation, Friends of
DFCI and Claudia
Adams Barr Program. Latest updates 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. 12/14/07: (1) Start to add toolbar and menu icons. (2) R view is changed to an “R codes” dialog and the
Analysis view is used for R output. 12/7/07: “Tools/Gene list by keywords” can
accept a gene symbol file (each line for a gene) and convert
gene symbols to probe set names. 11/29/07: UPD
can be displayed in copy number summary plot. 11/22/07: Check “Chromosome/Show LOH in
Copy” to show uniparental disomy (UPD) in
black in inferred copy or log2 view. 11/19/07: Process
human gene ST array. 11/18/07: Sample correlation matrix is drawn in
the Plots view. When samples are clustered, the correlation matrix has the
same order. 10/10/07: (1) While in the chromosome
view, use "Chromosome/Sort Samples"
to sort samples according to the current SNP's data values under view. (2) Make SNP genome information files using a Python program. 10/7/07: Set
"Options/Chromosome/Fixed HMM SD" to be > 0 to use this value as
the standard deviation (SD) of copy number HMM's
emission distribution, instead of computing SDs
SNP-wise from normal samples. Larger values will lead to more smooth
HMM-inferred copy numbers. 10/3/07: Scale
inferred copy number by "mode copy number" to recover absolute
copy numbers. 9/15/07: Export SNP copy number or LOH data in UCSC Wiggle format. 8/25/07: "Chromosome/Export SNP
data" can export chromosome regions
for both inferred copy and LOH data, and for both single samples and summary
score (use key S to toggle). To compute
summary score for copy number data, set "Options/Threshold" to
be not equal to 2. 8/12/07: Chromosome region data can be exported to find genes or cytobands altered in high percentage of samples. |
