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Sample GSM334528 Query DataSets for GSM334528
Status Public on Dec 01, 2009
Title Case/control experiment: P.8.01449.274.QwF73.y.LSCC
Sample type RNA
 
Source name PBMC
Organism Homo sapiens
Characteristics Class: NSCLC
Patient.id: 1449
Smoking: Q
Race: w
Gender: F
Age: 73
COPD: y
Dx: LSCC
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.1449
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 272.601
ILMN_1746533 49.708
ILMN_1800540 4854.28
ILMN_1785340 125.301
ILMN_1779536 268.225
ILMN_1654552 1202.35
ILMN_1754400 337.148
ILMN_1654861 441.191
ILMN_1697268 3479.02
ILMN_1720430 456.74
ILMN_1665877 5287.06
ILMN_1789751 5599.64
ILMN_1876197 56.568
ILMN_1695763 102.667
ILMN_1751530 187.926
ILMN_1763386 969.25
ILMN_1786275 37.7765
ILMN_1730670 107.394
ILMN_1664644 822.811
ILMN_1714602 1256.88

Total number of rows: 15227

Table truncated, full table size 306 Kbytes.




Supplementary file Size Download File type/resource
GSM334528.txt.gz 502.0 Kb (ftp)(http) TXT
Processed data included within Sample table

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