NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM334616 Query DataSets for GSM334616
Status Public on Dec 01, 2009
Title Before vs after surgery experiment: P.3.01252.091.QwF65.n.AC
Sample type RNA
 
Source name PBMC
Organism Homo sapiens
Characteristics Class: PRE
Patient.id: 1252
Smoking: Q
Race: w
Gender: F
Age: 65
COPD: n
Dx: AC
Stage: 4
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
Before vs after surgery experiment
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 413.478
ILMN_1746533 52.745
ILMN_1800540 9551.7
ILMN_1785340 110.692
ILMN_1779536 139.842
ILMN_1654552 1004.83
ILMN_1754400 486.828
ILMN_1654861 692.623
ILMN_1697268 5140.58
ILMN_1720430 296.793
ILMN_1665877 7494.43
ILMN_1789751 4232.31
ILMN_1876197 36.544
ILMN_1695763 248.332
ILMN_1751530 104.726
ILMN_1763386 838.315
ILMN_1786275 31.0335
ILMN_1730670 150.042
ILMN_1664644 1376.66
ILMN_1714602 2019.19

Total number of rows: 15227

Table truncated, full table size 306 Kbytes.




Supplementary file Size Download File type/resource
GSM334616.txt.gz 496.4 Kb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap