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Sample GSM124961 Query DataSets for GSM124961
Status Public on Mar 29, 2007
Title Liver18_Cy3
Sample type RNA
 
Source name Normal liver tissue
Organism Homo sapiens
Characteristics Tissue: normal Liver
Biomaterial provider Faculdade de Medicina - University of Sao Paulo
Extracted molecule total RNA
Extraction protocol TRIZOL (Invitrogen) extraction
Label Cy3
Label protocol Low RNA Input Linear Amplification Kit (Agilent Technologies)
 
Hybridization protocol In situ Hybridization Kit Plus (Agilent Technologies)
Scan protocol GenePix 4000B microarray scanner (Axon Instruments)
Description Total RNA was treated with DNase I (RNeasy - Qiagen) before labeling
Data processing We employed in our analyses the Median-based Trimmed Mean density value (MTM) for each spot by Arrayvision. The reported value represents the mean of all the pixels remaining in a target, after first removing pixels with density values that exceed four median absolute deviations (MADs) above or below the median intensity of the target. This measure moderates the influence of image artifacts (e.g., dust particles) on density estimation. The MTM density for each spot was subtracted by the individual background surrounding the spot (size 4 pixels). Spot quantization matrixes (the �raw� output of the image analysis software) were obtained from all hybridizations. Measurements correspond to the raw data generated by the Image analysis software. We have consolidated in a single tab-delimited text file all measurements obtained in all hybridizations in order to facilitate subsequent normalization and averaging of signal intensities from each tissue. Microarray data intensities from spots representing controls were removed and raw quantization matrixes from each tissue samples were normalized using a robust locally weighted linear regression algorithm (lowess), implemented into the R package, to correct for systematic biases on the data originated from small differences in the labeling and/or detection efficiencies between the fluorescent dyes. Next, in order to make experiments comparable, expression profiles were scaled to a reference, based on the trimmed mean intensity of all intensities measured in each sample that were expressed in at least one tissue, where the highest and the lowest 20% of the values were excluded from the calculated mean. A parallel analysis was performed to detect spots with signal intensity above the detection cutoff, which was determined by the average intensity plus 2 standard-deviations of 1,198 negative controls present in microarray platform. The raw intensity of each spot was compared to the detection cutoff of the corresponding dye. A spot was considered �expressed� if all 4 signals from a tissue were above the detection cutoff. For statistical analyses, Significance Analysis of Microarray (SAM) approach was employed using as parameters: multi-class response, 1000 permutations, K-Nearest Neighbors Imputer, and false discovery rate (FDR)  0.00001%; analysis of variance (ANOVA) implemented in the SpotFire Decision Site for Functional Genomics (SpotFire Inc.) with a cutoff of p less than 0.001. Gene sets identified by both SAM and ANOVA were combined in order to identify a more restrict set of spots that showed statistically significant expression changes in a tissue by both analyses.
 
Submission date Aug 03, 2006
Last update date Mar 29, 2007
Contact name Helder I. Nakaya
E-mail(s) hnakaya@usp.br
Phone +551126481130
Organization name Universidade de São Paulo
Lab csbiology.com
Street address AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17
City SÃO PAULO
State/province SÃO PAULO
ZIP/Postal code 05508000
Country Brazil
 
Platform ID GPL4051
Series (1)
GSE5452 Tissue-specific signature

Data table header descriptions
ID_REF
Liver18-Cy3-raw_data Raw data - Background-subtracted Median-based Trimmed Mean density value (MTM) extracted from Arrayvision software (Version 8.0, Imaging Research Inc.)
VALUE Normalized data from normal liver tissue sample

Data table
ID_REF Liver18-Cy3-raw_data VALUE
1 10.979 null
2 16.157 null
3 5.813 null
4 null null
5 null null
6 14.612 38.5693312
7 1.68 4.434470053
8 85.883 226.6938045
9 15.854 41.84767156
10 552.531 1458.44177
11 null null
12 34.751 91.72754097
13 3.246 null
14 12.898 34.04511592
15 29.202 77.08059196
16 null null
17 6.196 16.35474789
18 null null
19 26.386 69.64757549
20 10.087 26.62529728

Total number of rows: 44290

Table truncated, full table size 966 Kbytes.




Supplementary data files not provided

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