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Sample GSM96010 Query DataSets for GSM96010
Status Public on Feb 25, 2006
Title Ovarian Cell Line OVCA429
Sample type RNA
 
Channel 1
Source name CRD Reference
Organism Homo sapiens
Characteristics CRD Reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Ovarian Cell Line OV413
Organism Homo sapiens
Characteristics Ovarian Cell Line OV413
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5910.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Feb 07, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL178
Series (1)
GSE4197 Ovarian cell lines

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_MEAN Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_MEDIAN Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2B_MEDIAN Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1D_MEAN The mean feature pixel intensity with the median background subtracted (channel 1).; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN The mean feature pixel intensity with the median background subtracted (channel 2).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_MEAN Mean intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN Mean intensities of background pixels of Cy5.; Type: integer; Scale: linear_scale; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PIX_RAT2_MEDIAN Contains median of Ch2PI-CH2B/Ch1PI-CH1B where Ch1PI & Ch2PI represent single pixel intensities.; Type: float; Scale: linear_scale
TOT_SPIX Count of the number of pixels in the spot.; Type: integer; Scale: linear_scale
TOT_BPIX Number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG User defined spot flag (default 0).; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
VALUE Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1B_MEAN CH2B_MEAN PERGTBCH1I_1SD PERGTBCH2I_1SD PIX_RAT2_MEDIAN TOT_SPIX TOT_BPIX REGR CORR TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN RAT1N_MEAN VALUE
1 1122 1992 124 59 998 1933 166 148 69 70 1.717 112 1233 1.851 .907 80 92 65 77 0 1992 59 1933 1.937 .516 .954
2 995 1006 129 64 866 942 175 156 72 75 1.082 112 1017 1.042 .889 80 92 80 92 0 1006 64 942 1.088 .919 .121
3 996 1440 129 64 867 1376 153 101 80 84 1.565 112 1017 1.487 .924 80 92 95 107 0 1440 64 1376 1.587 .63 .666
4 781 555 126 64 655 491 142 81 81 83 .724 112 1017 .697 .906 80 92 110 122 0 555 64 491 .75 1.334 -.416
5 1819 1023 130 63 1689 960 149 78 86 84 .569 112 1017 .516 .917 80 92 125 137 0 1023 63 960 .568 1.759 -.815
6 1827 1745 131 65 1696 1680 150 77 95 89 1.005 112 1017 .956 .951 80 92 140 152 0 1745 65 1680 .991 1.01 -.014
7 977 1085 129 66 848 1019 142 75 70 81 1.125 112 1017 1.043 .905 80 92 155 167 0 1085 66 1019 1.202 .832 .265
8 870 861 129 67 741 794 188 162 75 78 1.036 112 1017 1.178 .941 80 92 170 182 0 861 67 794 1.072 .933 .1
9 4680 7204 132 68 4548 7136 199 173 83 90 1.46 112 1017 1.47 .927 80 92 185 197 0 7204 68 7136 1.569 .637 .65
10 1248 606 133 69 1115 537 199 164 79 75 .452 112 1017 .789 .826 80 92 200 212 0 606 69 537 .482 2.076 -1.054
11 834 543 133 69 701 474 150 132 78 85 .66 112 1017 .656 .587 80 92 215 227 0 543 69 474 .676 1.479 -.565
12 1860 9183 133 70 1727 9113 152 146 75 89 5.219 112 1017 4.841 .952 80 92 230 242 0 9183 70 9113 5.277 .19 2.4
13 1260 1434 131 70 1129 1364 167 122 73 83 1.139 112 1017 1.054 .88 80 92 245 257 0 1434 70 1364 1.208 .828 .273
14 6016 7905 129 67 5887 7838 164 105 83 86 1.37 112 1017 1.235 .944 80 92 260 272 0 7905 67 7838 1.331 .751 .413
15 821 970 127 64 694 906 146 83 71 77 1.135 112 1017 1.154 .907 80 92 275 287 0 970 64 906 1.305 .766 .385
16 1478 2399 128 64 1350 2335 179 94 70 80 1.677 112 1017 1.489 .912 80 92 290 302 0 2399 64 2335 1.73 .578 .79
17 5301 5683 136 68 5165 5615 594 506 83 91 1.05 112 1013 .982 .951 80 92 304 316 0 5683 68 5615 1.087 .92 .121
18 664 419 154 80 510 339 892 851 80 71 .575 112 1017 1.011 .961 80 92 319 331 0 419 80 339 .665 1.504 -.589
19 3705 6346 153 81 3552 6265 868 842 77 86 1.672 112 1013 1.343 .909 80 92 334 346 0 6346 81 6265 1.764 .567 .819
20 1411 2046 136 70 1275 1976 235 204 80 85 1.558 112 1013 1.342 .929 80 92 349 361 0 2046 70 1976 1.55 .645 .632

Total number of rows: 24192

Table truncated, full table size 2682 Kbytes.




Supplementary data files not provided
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