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Sample GSM96030 Query DataSets for GSM96030
Status Public on Feb 25, 2006
Title Ovarian Ca OV410
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 OV410
Organism Homo sapiens
Characteristics Ovarian Ca OV410
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5517.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 1020 1394 76 138 944 1256 95 152 84 88 1.296 112 1237 1.22 .906 91 103 58 70 0 1269 126 1143 1.211 .826 .277 .277
2 1011 968 80 143 931 825 123 167 88 89 .898 112 1021 .764 .893 90 102 73 85 0 881 130 751 .807 1.24 -.31 -.31
3 764 654 82 147 682 507 111 165 83 82 .663 112 1021 .627 .81 90 102 88 100 0 595 134 462 .677 1.478 -.563 -.563
4 546 570 86 151 460 419 106 168 83 83 .889 112 1025 .772 .822 90 102 104 116 0 519 137 381 .829 1.206 -.27 -.27
5 1547 1077 89 154 1458 923 108 170 90 89 .659 112 1017 .537 .881 90 102 119 131 0 980 140 840 .576 1.735 -.795 -.795
6 1456 1891 88 150 1368 1741 108 178 91 92 1.233 112 1017 1.147 .915 90 102 134 146 0 1722 137 1585 1.159 .863 .212 .212
7 820 766 88 150 732 616 111 181 70 66 .941 112 1017 .728 .858 90 102 149 161 0 697 137 561 .766 1.305 -.384 -.384
8 797 4417 86 150 711 4267 125 177 83 92 6.056 112 1017 3.83 .756 90 102 164 176 0 4021 137 3885 5.464 .183 2.45 2.45
9 6375 3630 85 149 6290 3481 132 189 83 86 .579 112 1017 .474 .882 90 102 179 191 0 3305 136 3169 .504 1.985 -.989 -.989
10 1182 951 84 150 1098 801 142 289 78 75 .719 112 1021 .832 .526 89 101 194 206 0 866 137 729 .664 1.506 -.59 -.59
11 737 826 83 153 654 673 124 297 75 83 1.019 112 1017 1.536 .578 89 101 209 221 0 752 139 613 .937 1.067 -.094 -.094
12 1720 1772 84 155 1636 1617 128 296 83 89 1.027 112 1017 .953 .693 89 101 224 236 0 1613 141 1472 .9 1.111 -.152 -.152
13 1092 1529 83 156 1009 1373 136 217 68 71 1.373 112 1017 1.166 .885 89 101 239 251 0 1392 142 1250 1.239 .807 .309 .309
14 5728 3921 86 154 5642 3767 138 211 87 91 .65 112 1017 .607 .906 89 101 254 266 0 3570 140 3429 .608 1.645 -.718 -.718
15 701 3708 83 152 618 3556 129 197 85 96 5.248 112 1017 4.453 .838 89 101 269 281 0 3376 138 3237 5.238 .191 2.389 2.389
16 1120 1734 83 151 1037 1583 136 193 77 83 1.439 112 1017 1.25 .871 89 101 284 296 0 1579 137 1441 1.39 .72 .475 .475
17 4765 2622 82 152 4683 2470 134 175 87 89 .535 112 1017 .465 .914 89 101 299 311 0 2387 138 2249 .48 2.083 -1.058 -1.058
18 557 788 81 156 476 632 125 177 83 76 1.225 112 1021 .841 .724 88 100 314 326 0 717 142 575 1.209 .827 .274 .274
19 2995 4601 80 154 2915 4447 91 167 92 92 1.514 112 1017 1.352 .894 88 100 329 341 0 4189 140 4048 1.389 .72 .474 .474
20 1077 1776 83 153 994 1623 98 174 80 85 1.719 112 1017 1.465 .913 88 100 344 356 0 1617 139 1478 1.486 .673 .572 .572

Total number of rows: 24192

Table truncated, full table size 2837 Kbytes.




Supplementary data files not provided

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