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Sample GSM96032 Query DataSets for GSM96032
Status Public on Feb 25, 2006
Title Ovarian Ca OV420
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 OV420
Organism Homo sapiens
Characteristics Ovarian Ca OV420
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Solid tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7423.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) [email protected]
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 GPL2936
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
1 910 1287 182 162 728 1125 187 166 66 73 1.489 112 1233 1.442 .955 105 117 72 84 0 1237 155 1082 1.486 .673 .572 .572
2 706 1154 180 159 526 995 189 166 61 67 1.932 112 1021 1.716 .962 104 116 87 99 0 1109 152 957 1.819 .55 .863 .863
3 761 463 184 165 577 298 192 172 61 57 .548 112 1017 .492 .941 104 116 102 114 0 445 158 287 .497 2.01 -1.008 -1.008
4 436 475 189 170 247 305 199 177 53 55 1.303 112 1017 1.097 .887 104 116 117 129 0 456 163 293 1.186 .843 .246 .246
5 1891 602 188 169 1703 433 198 174 78 68 .263 112 1025 .25 .961 103 115 132 144 0 578 162 416 .244 4.094 -2.033 -2.033
6 929 1036 190 170 739 866 201 175 66 71 1.157 112 1021 1.099 .957 103 115 147 159 0 996 163 833 1.127 .887 .173 .173
7 449 320 190 169 259 151 198 172 49 41 .641 112 1017 .57 .881 103 115 162 174 0 307 162 145 .56 1.786 -.837 -.837
8 405 518 193 169 212 349 202 178 48 57 1.733 112 1017 1.454 .92 103 115 177 189 0 498 162 336 1.585 .631 .664 .664
9 5526 4483 193 168 5333 4315 200 174 71 76 .798 112 1021 .792 .986 102 114 192 204 0 4310 161 4149 .778 1.285 -.362 -.362
10 785 264 192 166 593 98 198 172 61 43 .181 112 1017 .168 .824 102 114 207 219 0 253 159 94 .159 6.309 -2.657 -2.657
11 489 494 188 165 301 329 195 172 58 66 1.088 112 1021 .936 .917 102 114 222 234 0 475 158 317 1.053 .95 .075 .075
12 1606 2280 188 166 1418 2114 200 181 73 77 1.478 112 1021 1.405 .971 102 114 237 249 0 2192 159 2033 1.434 .697 .52 .52
13 1061 1389 192 168 869 1221 211 188 66 75 1.405 112 1021 1.301 .96 101 113 252 264 0 1335 161 1174 1.351 .74 .434 .434
14 9342 6085 191 172 9151 5913 205 182 88 89 .654 112 1017 .622 .982 101 113 267 279 0 5850 165 5685 .621 1.61 -.687 -.687
15 670 511 191 170 479 341 204 178 74 72 .729 112 1021 .642 .924 101 113 282 294 0 491 163 328 .685 1.46 -.546 -.546
16 891 552 192 169 699 383 197 173 61 63 .562 112 1025 .51 .963 101 113 298 310 0 530 162 368 .526 1.899 -.926 -.926
17 5475 2247 192 167 5283 2080 197 172 80 79 .403 112 1021 .38 .978 100 112 313 325 0 2160 160 2000 .379 2.642 -1.401 -1.401
18 359 437 190 164 169 273 195 168 46 59 1.615 112 1017 1.302 .874 100 112 328 340 0 420 157 263 1.556 .643 .638 .638
19 2184 3716 186 162 1998 3554 189 166 69 76 1.757 112 1017 1.709 .98 100 112 343 355 0 3573 155 3418 1.711 .585 .775 .775
20 756 767 184 162 572 605 187 166 66 67 1.069 112 1017 .975 .94 100 112 358 370 0 737 155 582 1.017 .983 .025 .025

Total number of rows: 24192

Table truncated, full table size 2848 Kbytes.




Supplementary data files not provided
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