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Sample GSM96020 Query DataSets for GSM96020
Status Public on Feb 25, 2006
Title Ovarian Ca OV408
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 Ca OV408
Organism Homo sapiens
Characteristics Ovarian Ca OV408
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Solid tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/4060.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 (2)
GSE4198 Ovarian cancers
GSE4268 Breast and ovarian carcinoma

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 same as UNF_VALUE but with flagged values removed
UNF_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 UNF_VALUE
1 605 764 81 131 524 633 91 166 70 69 1.14 112 1233 1.065 .822 68 80 104 116 0 741 127 614 1.172 .853 .229 .229
2 626 863 84 138 542 725 101 183 65 54 1.31 112 1025 1.167 .814 67 79 119 131 0 837 133 704 1.299 .77 .377 .377
3 553 480 84 141 469 339 99 171 68 62 .713 112 1021 .68 .803 67 79 134 146 0 466 136 330 .704 1.421 -.507 -.507
4 309 304 84 138 225 166 104 162 66 58 .789 112 1017 .65 .681 67 79 149 161 0 295 133 162 .72 1.389 -.474 -.474
5 1050 365 85 137 965 228 105 160 76 62 .243 112 1017 .219 .771 67 79 164 176 0 354 133 221 .229 4.367 -2.126 -2.126
6 505 444 87 137 418 307 104 158 69 66 .745 112 1017 .662 .747 67 79 179 191 0 431 133 298 .713 1.403 -.488 -.488
7 308 311 87 137 221 174 96 151 63 55 .811 112 1017 .608 .712 67 79 194 206 0 301 133 168 .76 1.315 -.396 -.396
8 275 281 87 141 188 140 123 186 64 51 .79 112 1017 .562 .701 67 79 209 221 0 272 136 136 .723 1.382 -.467 -.467
9 2477 1113 85 141 2392 972 125 189 72 61 .373 112 1017 .353 .784 67 79 224 236 0 1080 136 944 .395 2.534 -1.341 -1.341
10 534 269 87 144 447 125 115 180 74 54 .292 112 1017 .307 .624 67 79 239 251 0 261 139 122 .273 3.664 -1.873 -1.873
11 323 295 86 144 237 151 94 158 72 60 .686 112 1017 .551 .679 67 79 254 266 0 286 139 147 .62 1.612 -.689 -.689
12 992 840 88 146 904 694 107 172 80 75 .719 112 1017 .634 .797 67 79 269 281 0 815 141 674 .746 1.341 -.424 -.424
13 438 359 87 144 351 215 129 225 74 59 .634 112 1017 .764 .628 67 79 284 296 0 348 139 209 .595 1.679 -.748 -.748
14 3999 3810 91 145 3908 3665 133 225 84 75 .889 112 1017 .824 .807 67 79 299 311 0 3699 140 3559 .911 1.098 -.135 -.135
15 366 516 91 143 275 373 121 210 75 74 1.444 112 1017 1.178 .682 67 79 314 326 0 500 138 362 1.316 .76 .397 .397
16 566 445 89 145 477 300 106 163 78 66 .659 112 1017 .511 .727 67 79 329 341 0 432 140 292 .612 1.634 -.708 -.708
17 2964 1622 87 142 2877 1480 107 157 92 83 .514 112 1017 .383 .732 67 79 344 356 0 1574 137 1437 .499 2.002 -1.002 -1.002
18 287 317 87 142 200 175 112 176 72 65 .946 112 1017 .568 .499 67 79 359 371 0 307 137 170 .85 1.176 -.234 -.234
19 971 1968 87 144 884 1824 109 185 73 76 1.98 112 1017 1.615 .784 67 79 374 386 0 1910 139 1771 2.003 .499 1.002 1.002
20 492 663 89 149 403 514 112 193 71 75 1.24 112 1017 1.038 .746 67 79 389 401 0 643 144 499 1.238 .808 .308 .308

Total number of rows: 24192

Table truncated, full table size 2819 Kbytes.




Supplementary data files not provided
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