|
| Status |
Public on Dec 03, 2009 |
| Title |
7201_Match_1 (Agilent 251469334156) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Breast carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
sample: 7201T
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
standard Agilent protocol
|
| Label |
Cy5
|
| Label protocol |
standard Agilent protocol
|
| |
|
| Channel 2 |
| Source name |
Matched Normal
|
| Organism |
Homo sapiens |
| Characteristics |
sample: 7201N
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
standard Agilent protocol
|
| Label |
Cy3
|
| Label protocol |
standard Agilent protocol
|
| |
|
| |
| Hybridization protocol |
standard Agilent protocol
|
| Scan protocol |
standard Agilent protocol
|
| Description |
Genomic DNA extracted from breast tumors was was interrogated for copy number against matched normal genomic DNA on the Agilent Human Genome CGH Microarray Kit 244A.
|
| Data processing |
Data were processed from raw text files using R and limma (using limma's “agilent” source option). Probes apparently not 60 bases in length were removed and arrays were normalized using the normexp deconvolution background correction method and loess regression of log-ratios to remove dye-bias.
|
| |
|
| Submission date |
Dec 02, 2009 |
| Last update date |
Dec 02, 2009 |
| Contact name |
Christina Curtis |
| E-mail(s) |
christina.curtis@cancer.org.uk
|
| Phone |
01223404231
|
| Fax |
1223 404208
|
| Organization name |
University of Cambridge
|
| Department |
Computational Biology/Oncology
|
| Lab |
Tavaré
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB20RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL4091 |
| Series (1) |
| GSE16400 |
The pitfalls of platform comparison: DNA copy number array technologies assessed |
|
