NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM96027 Query DataSets for GSM96027
Status Public on Feb 25, 2006
Title Ovarian Ca OV98B
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 OV98B
Organism Homo sapiens
Characteristics Ovarian Ca OV98B
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Ascites, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/4068.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 1010 1092 140 175 870 917 180 225 66 62 1.091 112 1269 .957 .84 56 68 65 77 0 1790 286 1504 1.729 .578 .79 .79
2 1097 1239 138 173 959 1066 185 240 68 68 1.12 112 1061 .948 .839 56 68 80 92 0 2031 283 1748 1.823 .549 .866 .866
3 851 832 136 169 715 663 158 204 72 66 .998 112 1061 .712 .747 56 68 95 107 0 1363 277 1086 1.519 .658 .603 .603
4 477 337 136 169 341 168 154 194 73 59 .579 112 1061 .474 .683 56 68 110 122 0 552 277 275 .806 1.24 -.31 -.31
5 1639 431 137 172 1502 259 163 205 75 64 .185 112 1061 .15 .653 56 68 125 137 0 706 281 425 .283 3.534 -1.821 -1.821
6 1042 1224 136 166 906 1058 163 205 100 97 1.109 112 1061 1.143 .842 56 68 140 152 0 2006 272 1734 1.914 .522 .937 .937
7 987 787 135 162 852 625 151 199 60 52 1.048 112 1061 .332 .739 56 68 155 167 0 1290 265 1025 1.203 .831 .267 .267
8 585 867 137 164 448 703 166 215 63 69 1.647 112 1061 1.123 .759 56 68 170 182 0 1421 268 1153 2.574 .389 1.364 1.364
9 5761 2375 139 167 5622 2208 178 214 71 69 .418 112 1053 .378 .89 56 68 185 197 0 3893 273 3620 .644 1.553 -.635 -.635
10 972 507 136 166 836 341 179 227 71 58 .394 112 1053 .355 .601 56 68 200 212 0 831 272 559 .669 1.496 -.581 -.581
11 628 1255 134 164 494 1091 152 210 67 65 1.988 112 1053 1.608 .75 56 68 215 227 0 2057 268 1789 3.621 .276 1.857 1.857
12 1530 2103 136 163 1394 1940 155 213 78 70 1.346 112 1053 1.138 .768 56 68 230 242 0 3447 267 3180 2.281 .438 1.19 1.19
13 800 730 136 167 664 563 184 256 64 65 .871 112 1053 .685 .695 56 68 245 257 0 1196 273 923 1.39 .719 .475 .475
14 5205 3759 138 168 5067 3591 198 251 78 68 .712 112 1053 .59 .749 56 68 260 272 0 6162 275 5887 1.162 .861 .216 .216
15 530 504 138 168 392 336 195 246 74 63 .847 112 1053 .702 .643 56 68 275 287 0 826 275 551 1.406 .711 .491 .491
16 896 666 139 163 757 503 164 203 73 63 .656 112 1053 .599 .767 56 68 290 302 0 1091 267 824 1.089 .919 .122 .122
17 4857 2356 142 170 4715 2186 173 213 83 75 .477 112 1053 .417 .832 56 68 305 317 0 3862 278 3584 .76 1.316 -.396 -.396
18 370 677 143 169 227 508 179 242 63 60 2.116 112 1057 1.264 .691 56 68 319 331 0 1109 277 832 3.665 .273 1.874 1.874
19 2129 2543 143 176 1986 2367 163 239 74 71 1.25 112 1061 1.01 .796 56 68 334 346 0 4168 288 3880 1.954 .512 .966 .966
20 735 788 148 189 587 599 177 297 66 64 1.206 112 1073 .879 .433 56 68 349 361 0 1291 309 982 1.673 .598 .742 .742

Total number of rows: 24192

Table truncated, full table size 2817 Kbytes.




Supplementary data files not provided

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