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Sample GSM96029 Query DataSets for GSM96029
Status Public on Feb 25, 2006
Title Ovarian Ca OV308
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 OV308
Organism Homo sapiens
Characteristics Ovarian Ca OV308
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Ascites, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/4337.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 1245 1464 131 101 1114 1363 140 107 82 83 1.175 112 1233 1.069 .89 122 134 78 90 0 2005 138 1867 1.676 .597 .745 .745
2 1288 1212 133 102 1155 1110 147 109 76 83 .948 112 1017 .862 .918 122 134 93 105 0 1660 139 1521 1.317 .759 .397 .397
3 908 835 135 102 773 733 142 106 79 83 .874 112 1017 .795 .875 122 134 108 120 0 1143 139 1004 1.299 .77 .377 .377
4 519 274 134 102 385 172 136 104 82 82 .434 112 1017 .363 .802 122 134 123 135 0 375 139 236 .613 1.631 -.706 -.706
5 1959 517 135 103 1824 414 141 106 88 83 .218 112 1017 .187 .836 122 134 138 150 0 708 141 567 .311 3.217 -1.686 -1.686
6 1197 945 138 106 1059 839 144 108 98 91 .752 112 1017 .734 .893 122 134 153 165 0 1294 145 1149 1.085 .922 .118 .118
7 580 369 138 105 442 264 143 108 63 66 .587 112 1017 .498 .87 123 135 168 180 0 505 143 362 .819 1.221 -.288 -.288
8 610 373 136 106 474 267 145 111 68 66 .564 112 1021 .483 .857 123 135 183 195 0 510 145 365 .77 1.299 -.377 -.377
9 6243 1513 135 109 6108 1404 150 116 75 75 .232 112 1025 .204 .895 123 135 198 210 0 2072 149 1923 .315 3.176 -1.667 -1.667
10 937 301 137 109 800 192 148 116 66 65 .238 112 1025 .194 .8 123 135 214 226 0 412 149 263 .329 3.042 -1.605 -1.605
11 614 1372 138 106 476 1266 146 121 72 79 2.44 112 1017 2.257 .893 123 135 229 241 0 1879 145 1734 3.643 .275 1.865 1.865
12 1716 4602 139 104 1577 4498 147 119 76 87 2.52 112 1017 2.338 .875 123 135 244 256 0 6304 142 6162 3.907 .256 1.966 1.966
13 963 660 142 104 821 556 157 114 66 66 .662 112 1017 .578 .883 123 135 259 271 0 904 142 762 .928 1.077 -.108 -.108
14 6496 3496 143 102 6353 3394 156 110 86 88 .513 112 1017 .463 .888 123 135 274 286 0 4789 139 4650 .732 1.366 -.45 -.45
15 626 431 143 102 483 329 146 105 74 80 .631 112 1017 .572 .86 123 135 289 301 0 590 139 451 .934 1.071 -.099 -.099
16 1171 768 142 101 1029 667 153 106 78 76 .592 112 1017 .554 .883 123 135 304 316 0 1052 138 914 .888 1.126 -.171 -.171
17 5251 2167 141 103 5110 2064 152 107 86 89 .37 112 1017 .362 .901 123 135 319 331 0 2968 141 2827 .553 1.808 -.854 -.854
18 424 261 139 106 285 155 153 115 67 66 .532 112 1017 .469 .8 123 135 334 346 0 357 145 212 .744 1.344 -.427 -.427
19 2583 2648 138 110 2445 2538 147 117 77 80 .947 112 1017 .916 .92 123 135 349 361 0 3627 150 3477 1.422 .703 .508 .508
20 941 577 138 110 803 467 148 117 72 75 .559 112 1017 .508 .907 123 135 364 376 0 790 150 640 .797 1.255 -.327 -.327

Total number of rows: 24192

Table truncated, full table size 2860 Kbytes.




Supplementary data files not provided
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