How to cite dChip etc?

[Henrik Bengtsson]

Hi,

Q1. How do prefer to cite the dChip *software*?

Q2. What is the difference between the dChipSNP and dChip software?
Is dChipSNP incorporated in dChip now? Is the dChipSNP executable
[downloadable from http://biosun1.harvard.edu/complab/dchip/snp/]
obsolete?

Q3. When doing total CN analysis/preprocessing using the methods in
dChip, what should be cited?

Q4. When doing allele-specific CN analysis/preprocessing using the
methods in dChip, what should be cited?

Thanks

Henrik

[Cheng Li]

Henrik,

There are two main references:

1. Cheng Li and Wing Hung Wong (2001) Model-based analysis of
oligonucleotide arrays: Expression index computation and outlier
detection, Proc. Natl. Acad. Sci. Vol. 98, 31-36.

2. Ming Lin, Lee-Jen Wei, William R. Sellers, Marshall Lieberfarb,
Wing Hung Wong*, and Cheng Li* (2004) dChipSNP: Significance Curve and
Clustering of SNP-Array-Based Loss-of-Heterozygosity Data.
Bioinformatics. 20: 1233-1240.

> Q1. How do prefer to cite the dChip *software*?

Either Ref 1 or 2. 2 if dChip SNP functions are used.

> Q2. What is the difference between the dChipSNP and dChip software?

They are the same. dChipSNP refers to dChip's SNP functions.

> Is dChipSNP incorporated in dChip now?

Yes.

> Is the dChipSNP executable
[downloadable from http://biosun1.harvard.edu/complab/dchip/snp/]
obsolete?

Yes.

> Q3. When doing total CN analysis/preprocessing using the methods in
dChip, what should be cited?

Ref 2.

> Q4. When doing allele-specific CN analysis/preprocessing using the
methods in dChip, what should be cited?

Cheng Li, Rameen Beroukhim, Barbara A. Weir, Wendy Winckler, Levi A.
Garraway, William R. Sellers, Matthew Meyerson (2008) Major copy
proportion analysis of tumor samples using SNP arrays. BMC
Bioinformatics. 9:204.

Thank you.

Cheng

Hi,

Thanks

Henrik

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