NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM96012 Query DataSets for GSM96012
Status Public on Feb 25, 2006
Title Ovarian Cell Line OVCA_8
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 MES-OV
Organism Homo sapiens
Characteristics Ovarian Ca MES-OV
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/4681.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 1125 1949 147 43 978 1906 185 104 86 94 1.939 112 1062 1.698 .866 90 102 47 59 0 2266 50 2216 2.266 .441 1.18
2 1373 1700 152 48 1221 1652 250 187 85 93 1.316 112 689 1.201 .873 90 102 62 74 0 1976 55 1921 1.573 .636 .654
3 806 1127 150 46 656 1081 224 133 71 87 1.513 112 618 1.24 .833 90 102 77 89 0 1310 53 1257 1.916 .522 .938
4 460 252 145 43 315 209 184 93 79 89 .62 112 617 .644 .753 90 102 93 105 0 293 50 243 .771 1.296 -.374
5 1301 375 144 43 1157 332 180 75 84 91 .284 112 615 .233 .794 90 102 108 120 0 436 50 386 .334 2.997 -1.584
6 1189 1059 146 46 1043 1013 184 72 92 100 .951 112 615 .824 .891 90 102 123 135 0 1231 53 1178 1.129 .885 .176
7 446 414 152 48 294 366 188 79 58 76 1.139 112 603 .938 .831 90 102 138 150 0 481 55 426 1.449 .69 .535
8 424 318 154 49 270 269 175 73 67 82 .864 112 594 .767 .814 90 102 153 165 0 369 56 313 1.159 .863 .213
9 2265 4458 154 46 2111 4412 181 77 80 98 1.953 112 600 1.795 .831 90 102 168 180 0 5183 53 5130 2.43 .412 1.281
10 1026 206 151 44 875 162 175 93 77 78 .174 112 600 .157 .358 90 102 183 195 0 239 51 188 .215 4.654 -2.219
11 544 150 150 45 394 105 180 132 69 75 .257 112 606 .416 .325 90 102 198 210 0 174 52 122 .31 3.23 -1.691
12 1716 4281 154 50 1562 4231 187 150 77 93 2.706 112 615 2.336 .874 90 102 213 225 0 4977 58 4919 3.149 .318 1.655
13 1093 1611 155 54 938 1557 197 121 72 83 1.581 112 624 1.375 .818 90 102 228 240 0 1873 62 1811 1.931 .518 .949
14 4811 8362 154 56 4657 8306 186 104 85 94 1.766 112 618 1.506 .861 90 102 243 255 0 9723 65 9658 2.074 .482 1.052
15 651 457 155 56 496 401 204 96 77 89 .763 112 622 .557 .745 90 102 258 270 0 531 65 466 .94 1.064 -.09
16 1300 529 156 56 1144 473 212 101 77 78 .398 112 613 .339 .736 90 102 273 285 0 615 65 550 .481 2.08 -1.057
17 3217 11381 156 53 3061 11328 203 91 86 95 3.625 112 606 3.153 .875 90 102 288 300 0 13233 61 13172 4.303 .232 2.105
18 421 220 153 50 268 170 180 90 66 82 .585 112 609 .872 .753 90 102 303 315 0 255 58 197 .735 1.36 -.444
19 2072 4288 151 47 1921 4241 166 73 85 94 2.115 112 618 1.904 .883 90 102 318 330 0 4986 54 4932 2.567 .389 1.36
20 1146 1865 150 47 996 1818 272 99 85 94 1.823 112 623 .251 .367 90 102 333 345 0 2168 54 2114 2.122 .471 1.086

Total number of rows: 24192

Table truncated, full table size 2614 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap