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Sample GSM334489 Query DataSets for GSM334489
Status Public on Dec 01, 2009
Title Case/control experiment: P.10.01307.319.QwM69.n.AC
Sample type RNA
 
Source name PBMC
Organism Homo sapiens
Characteristics Class: NSCLC
Patient.id: 1307
Smoking: Q
Race: w
Gender: M
Age: 69
COPD: n
Dx: AC
Stage: 1A
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.1307
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 538.464
ILMN_1746533 42.377
ILMN_1800540 3341.6
ILMN_1785340 84
ILMN_1779536 207.313
ILMN_1654552 1053.75
ILMN_1754400 492.149
ILMN_1654861 592.959
ILMN_1697268 3741.17
ILMN_1720430 327.749
ILMN_1665877 5741.87
ILMN_1789751 4241.2
ILMN_1876197 42.822
ILMN_1695763 121.316
ILMN_1751530 146.029
ILMN_1763386 1173.9
ILMN_1786275 53.367
ILMN_1730670 94.873
ILMN_1664644 1083.44
ILMN_1714602 1952.83

Total number of rows: 15227

Table truncated, full table size 306 Kbytes.




Supplementary file Size Download File type/resource
GSM334489.txt.gz 496.3 Kb (ftp)(http) TXT
Processed data included within Sample table

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