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Sample GSM79999 Query DataSets for GSM79999
Status Public on Oct 25, 2005
Title WT vs lpz8 null cells in low Cu
Sample type RNA
 
Channel 1
Source name WT
Organism Saccharomyces cerevisiae
Characteristics WT
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name lpz8 null cells in low Cu
Organism Saccharomyces cerevisiae
Characteristics lpz8 null cells in low Cu
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Metals, Copper
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/3022.gif
Data processing LOG_RAT2N_MEDIAN is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Oct 24, 2005
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 GPL65
Series (1)
GSE3502 Haa1 regulated transcription

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
1 647 958 369 708 278 250 379 719 58 32 .974 208 1123 .88 .715 96 112 136 152 0 529 391 138 .496 2.015 -1.011
2 395 771 376 739 19 32 380 745 2 3 1.943 208 840 .064 .051 98 114 153 169 0 425 408 18 .929 1.076 -.106
3 813 1388 385 778 428 610 389 780 61 60 1.477 208 850 1.022 .755 98 114 170 186 0 766 429 337 .786 1.272 -.347
4 485 897 379 786 106 111 391 807 8 4 1.471 208 748 1.411 .662 99 115 189 205 0 495 434 61 .578 1.731 -.791
5 884 1444 389 801 495 643 395 817 53 49 1.386 343 718 .684 .535 96 117 204 225 0 797 442 355 .717 1.395 -.48
6 441 878 413 855 28 23 420 883 2 3 1.31 195 760 1.956 .605 99 115 223 239 0 484 472 13 .453 2.206 -1.142
7 427 861 422 874 5 null 428 877 0 0 1.243 208 897 .133 .082 99 115 241 257 0 475 482 -7 null null null
8 444 901 431 893 13 8 437 893 0 0 1.378 208 886 .131 .076 99 115 258 274 0 497 493 4 .34 2.945 -1.558
9 440 907 444 920 null null 448 924 0 0 1.674 208 887 .298 .162 99 115 275 291 0 500 508 -7 null null null
10 461 931 450 946 11 null 453 949 0 0 1.372 208 897 .118 .07 99 115 292 308 0 514 522 -8 null null null
11 462 944 455 952 7 null 458 957 0 0 1.308 208 903 .187 .098 99 115 309 325 0 521 525 -4 null null null
12 489 994 468 979 21 15 485 1012 1 1 1.393 208 904 .365 .253 99 115 326 342 0 548 540 8 .394 2.537 -1.343
13 525 1057 469 980 56 77 485 1013 10 1 1.578 208 894 .609 .422 99 115 343 359 0 583 541 42 .759 1.318 -.398
14 443 966 461 966 null null 466 976 0 0 2.386 208 936 .646 .377 99 115 360 376 0 533 533 0 null null null
15 461 1002 461 975 null 27 470 994 0 0 1.701 208 849 .808 .449 102 118 378 394 0 553 538 15 null null null
16 467 980 463 981 4 null 472 998 0 0 2.58 208 853 .815 .438 102 118 395 411 0 541 541 -1 null null null
17 467 1001 464 988 3 13 467 990 0 0 2 208 874 .006 .003 102 118 412 428 0 552 545 7 2.391 .418 1.258
18 463 989 467 990 null null 469 990 0 0 1.947 208 955 .139 .079 101 117 431 447 0 546 546 -1 null null null
19 469 983 471 989 null null 475 991 0 0 1.184 208 936 null null 101 117 448 464 0 542 546 -3 null null null
20 465 993 475 992 null 1 478 997 0 0 2.078 208 921 .112 .063 101 117 465 481 0 548 547 1 null null null

Total number of rows: 8832

Table truncated, full table size 1001 Kbytes.




Supplementary data files not provided
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