|
| Status |
Public on Jan 17, 2012 |
| Title |
162-3 |
| Sample type |
RNA |
| |
|
| Source name |
blood cells, after 6 weeks treatment with tibolone
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cells from whole blood
gender: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from whole blood using the PAXgene® Blood RNA Kit 50 (Qiagen ref.762174). The total RNA was cleaned and concentrated to obtain smaller elution volumes using RNeasy® MinElute (Qiagen cat 74204).
|
| Label |
biotin
|
| Label protocol |
Standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
Standard Affymetrix protocol
|
| Scan protocol |
Arrays were scanned using GeneChip ® Scanner 3000 (Affymetrix). Image analysis was performed using GeneChip ® Operating Software 1.4 (Affymetrix)
|
| Description |
treatment group 3
|
| Data processing |
The data were normalized using the farms package (Hochreiter 2006) in R (version 2.10.1), using the RMA (Irizarry 2003) method. Probes were summarized using the revised entrez-based probe annotation of Dai (Dai 2005, the package hgu133plus2hsentrezgcdf.db, version 12.1.0), and classified as informative or non-informative using the method of Talloen (Talloen 2007). Non-informative probe sets were discarded. The latter two methods reduced the number of probe sets from 54,675 on the original chip, to 17,788 after re-annotation, and to 3,640 after discarding non-informative probe sets (filtered data provided as a supplementary file on GSE24859). Differentially expressed probe sets were identified using the limma R package (Smyth 2004) by subtracting baseline measurement for each patient from the measurement at six weeks, and compare the resulting expression differences between patients with different treatments using limma's moderated t-test. P-values were corrected for multiple testing using the false discovery rate-controlling procedure of Benjamini and Hochberg (Benjamini 1995).
|
| |
|
| Submission date |
Oct 21, 2010 |
| Last update date |
Jan 17, 2012 |
| Contact name |
Anders Erik Astrup Dahm |
| E-mail(s) |
a.e.a.dahm@medisin.uio.no
|
| Organization name |
Oslo University Hospital
|
| Department |
Hematology
|
| Lab |
Center of Thrombosis and Hemostasis Research
|
| Street address |
Kirkeveien 166
|
| City |
Oslo |
| ZIP/Postal code |
0407 |
| Country |
Norway |
| |
|
| Platform ID |
GPL11084 |
| Series (1) |
| GSE24859 |
Expression data from healthy postmenopausal women on 4 different types of hormone therapy, the RET study |
|
