NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM96016 Query DataSets for GSM96016
Status Public on Feb 25, 2006
Title Ovarian Cell Line OVCAR-3
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 OVCAR-3
Organism Homo sapiens
Characteristics Ovarian Ca OVCAR-3
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-line, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/4325.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
1 711 653 116 191 595 462 174 230 75 76 .808 112 1233 .512 .911 91 103 80 92 0 1070 313 757 1.272 .786 .347
2 719 678 118 198 601 480 146 223 66 64 .744 112 1017 .474 .64 91 103 95 107 0 1111 324 787 1.309 .764 .389
3 402 392 117 198 285 194 126 218 55 58 .779 112 1017 .638 .794 91 103 110 122 0 642 324 318 1.116 .896 .158
4 283 288 117 198 166 90 123 209 60 41 .648 112 1017 .352 .534 91 103 125 137 0 472 324 148 .892 1.122 -.166
5 1215 897 117 197 1098 700 125 205 69 75 .649 112 1017 .613 .867 91 103 140 152 0 1470 322 1148 1.046 .956 .064
6 816 440 118 197 698 243 124 204 88 71 .367 112 1017 .316 .764 91 103 155 167 0 721 322 399 .572 1.749 -.807
7 283 280 119 197 164 83 124 206 49 38 .594 112 1009 .36 .551 91 103 169 181 0 459 322 137 .835 1.197 -.26
8 304 274 122 197 182 77 127 205 51 43 .411 112 1017 .263 .467 91 103 184 196 0 449 322 127 .698 1.433 -.519
9 5267 2116 124 196 5143 1920 129 203 77 70 .358 112 1017 .319 .877 91 103 199 211 0 3468 321 3147 .612 1.634 -.709
10 723 285 123 199 600 86 129 204 62 40 .18 112 1017 .109 .588 91 103 214 226 0 467 326 141 .235 4.255 -2.089
11 374 238 122 198 252 40 127 203 64 23 .265 112 1017 .178 .481 91 103 229 241 0 390 324 66 .262 3.818 -1.933
12 1605 2179 122 195 1483 1984 125 202 68 77 1.4 112 1017 1.156 .888 91 103 244 256 0 3572 319 3253 2.194 .456 1.133
13 634 415 118 199 516 216 124 212 64 55 .458 112 1017 .371 .732 91 103 259 271 0 680 326 354 .686 1.458 -.544
14 6064 2511 117 198 5947 2313 122 214 83 78 .38 112 1017 .34 .922 91 103 274 286 0 4116 324 3792 .638 1.568 -.649
15 379 269 111 198 268 71 114 211 75 34 .358 112 1017 .275 .373 91 103 289 301 0 440 324 116 .433 2.31 -1.208
16 686 314 109 197 577 117 108 205 72 47 .252 112 1017 .141 .562 91 103 304 316 0 514 322 192 .333 3.005 -1.587
17 2121 637 103 193 2018 444 105 201 48 48 .284 112 1017 .208 .838 91 103 319 331 -100 1044 316 728 .361 2.772 -1.471
18 107 211 110 189 null 22 109 197 12 14 .605 112 1017 .591 .769 92 104 334 346 -100 345 309 36 null null null
19 344 490 112 194 232 296 113 201 13 20 .611 112 1009 .861 .79 92 104 348 360 -100 803 318 485 2.091 .478 1.064
20 168 210 113 197 55 13 114 207 18 18 .329 112 1017 .248 .613 92 104 363 375 -100 344 322 22 .4 2.5 -1.322

Total number of rows: 24192

Table truncated, full table size 2724 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap