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Sample GSM90657 Query DataSets for GSM90657
Status Public on Jan 06, 2006
Title AR PBL (#30) vs pref
Sample type RNA
 
Channel 1
Source name PBL reference (pod7, no rejection)
Organism Homo sapiens
Characteristics PBL reference (pod7, no rejection)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name acute rejection kid tx PBL (pt. #30)
Organism Homo sapiens
Characteristics acute rejection kid tx PBL (pt. #30)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Kidney, Transplant
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/6820.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 Jan 04, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL3306
Series (1)
GSE3976 Molecular profiling of anemia in acute renal allograft rejection

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
1 748 964 544 728 204 236 null null 0 0 .87 null null 1.19 .44 46 54 70 78 0 598 452 146 .718 1.393 -.478
2 772 1147 520 720 252 427 null null 0 0 1.24 null null 2.7 .84 46 54 78 86 0 712 447 265 1.052 .951 .073
3 670 1045 504 712 166 333 null null 0 0 1.39 null null 2.78 .84 46 54 87 95 0 649 442 207 1.245 .803 .316
4 603 981 496 704 107 277 null null 0 0 1.29 null null 2.22 .69 46 54 96 104 0 609 437 172 1.607 .622 .684
5 646 1025 488 712 158 313 null null 0 0 .9 null null 2.36 .79 46 54 104 112 0 636 442 194 1.229 .813 .298
6 596 911 488 704 108 207 null null 0 0 1.18 null null 2.11 .86 46 54 113 121 -100 565 437 128 1.19 .841 .25
7 613 984 480 704 133 280 null null 0 0 1.45 null null 3.72 .75 46 54 122 130 -100 611 437 174 1.307 .765 .386
8 630 944 464 696 166 248 null null 0 0 1.11 null null 2.64 .85 46 54 131 139 0 586 432 154 .927 1.079 -.109
9 700 1302 464 696 236 606 null null 0 0 1.53 null null 4.75 .88 46 54 139 147 0 808 432 376 1.594 .628 .672
10 1047 1398 464 688 583 710 null null 0 0 .81 null null 1.69 .9 46 54 148 156 0 868 427 441 .756 1.323 -.404
11 715 1155 464 688 251 467 null null 0 0 1.13 null null 2.25 .86 46 54 157 165 -100 717 427 290 1.155 .866 .207
12 574 967 472 680 102 287 null null 0 0 1.44 null null 2.53 .84 46 54 166 174 0 600 422 178 1.746 .573 .804
13 758 1676 472 680 286 996 null null 0 0 1.87 null null 5.66 .96 46 54 174 182 0 1040 422 618 2.161 .463 1.112
14 944 1260 480 680 464 580 null null 0 0 .73 null null 1.86 .93 46 54 183 191 0 782 422 360 .776 1.289 -.366
15 1115 1185 480 680 635 505 null null 0 0 .58 null null 1.37 .9 46 54 192 200 0 735 422 313 .494 2.026 -1.019
16 830 1290 472 672 358 618 null null 0 0 .97 null null 2.97 .83 46 54 201 209 0 801 417 384 1.071 .933 .099
17 759 1237 472 680 287 557 null null 0 0 1.15 null null 2.95 .81 46 54 209 217 0 768 422 346 1.204 .83 .268
18 510 718 480 680 30 38 null null 0 0 .8 null null .38 .18 46 54 218 226 -100 446 422 24 .786 1.272 -.347
19 853 1078 480 680 373 398 null null 0 0 .73 null null 1.87 .97 46 54 227 235 -100 669 422 247 .662 1.51 -.595
20 841 1599 488 680 353 919 null null 0 0 1.87 null null 3.78 .87 46 54 236 244 0 992 422 570 1.616 .619 .692

Total number of rows: 9216

Table truncated, full table size 1015 Kbytes.




Supplementary data files not provided
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