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Sample GSM334575 Query DataSets for GSM334575
Status Public on Dec 01, 2009
Title Case/control experiment: P.2.01643.067.QwM67.y.AC
Sample type RNA
 
Source name PBMC
Organism Homo sapiens
Characteristics Class: NSCLC
Patient.id: 1643
Smoking: Q
Race: w
Gender: M
Age: 67
COPD: y
Dx: AC
Stage: 3B
Extracted molecule total RNA
Extraction protocol Illumina protocol
Label biotin
Label protocol Illumina protocol
 
Hybridization protocol Illumina protocol
Scan protocol Illumina protocol
Description CPT purified PBMC
Case/control experiment
NSCLC.1643
Data processing Expression levels and normalization. Samples were processed as mixed batches (total of 12 batches) of patients and controls and hybridized to the Illumina WG-6v2 human whole genome bead arrays. Raw data was processed by Bead Studio v. 3.0 software. Expression levels were exported for signal and negative control probes. The set of negative control probes was used to calculate average background level for further filtering and background subtraction steps. Average values of the signal probe expression data for the 137 patient (NSCLC) and 91 control (NHC) sample arrays were used as a base for normalization and all the arrays, including 18 PRE/18 POST samples and NYU samples, were quantile normalized against this base.
Array quality control. After each hybridization batch, we computed gene-wise global correlation as a median Spearman correlation across all pairs of microarrays from all batches using expression levels of all signal probes (>48K). Median absolute deviation of the global correlation was also calculated. Then for each microarray a median spearman correlation against all other arrays was computed. The arrays whose median correlation differs from global correlation more than 8 absolute deviations (threshold was picked empirically) were marked as outliers and were not used for further analysis.
 
Submission date Oct 17, 2008
Last update date Nov 23, 2009
Contact name Louise C Showe
E-mail(s) lshowe@wistar.org
Phone 215-898-3791
Organization name The Wistar Institute
Lab Dr. Louise Showe
Street address 3601 Spruce St
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL6102
Series (1)
GSE13255 Gene Expression Profiles in Peripheral Blood Mononuclear Cells Can Distinguish Patients with NonSmall Cell Lung Cancer.

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ILMN_1725528 410.066
ILMN_1746533 58.366
ILMN_1800540 2378.17
ILMN_1785340 98.956
ILMN_1779536 157.132
ILMN_1654552 908.859
ILMN_1754400 426.723
ILMN_1654861 663.131
ILMN_1697268 4250.71
ILMN_1720430 306.914
ILMN_1665877 4869.1
ILMN_1789751 3074.1
ILMN_1876197 33.5893
ILMN_1695763 182.377
ILMN_1751530 104.291
ILMN_1763386 1272.58
ILMN_1786275 17.8456
ILMN_1730670 93.217
ILMN_1664644 1482.64
ILMN_1714602 2219.65

Total number of rows: 15227

Table truncated, full table size 306 Kbytes.




Supplementary file Size Download File type/resource
GSM334575.txt.gz 497.4 Kb (ftp)(http) TXT
Processed data included within Sample table

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