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Sample GSM96006 Query DataSets for GSM96006
Status Public on Feb 08, 2006
Title 500 uM Fe vs 100 uM Fe: met
Sample type RNA
 
Channel 1
Source name 100 uM Fe
Organism Saccharomyces cerevisiae
Characteristics 100 uM Fe
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 500 uM Fe
Organism Saccharomyces cerevisiae
Characteristics 500 uM Fe
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/8695.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 GPL59
Series (1)
GSE4196 Iron uptake experiments in yeast

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 5849 3772 5268 2868 581 904 null null 0 0 null null null .23 .53 24 33 62 71 0 3117 2370 747 1.286 .778 .363
2 5775 3209 5268 2649 507 560 null null 0 0 null null null .78 .78 24 33 72 81 0 2652 2189 463 .913 1.095 -.131
3 5544 3102 5027 2591 517 511 null null 0 0 null null null .84 .79 24 33 82 91 0 2563 2141 422 .816 1.225 -.293
4 5650 3242 5084 2641 566 601 null null 0 0 null null null .9 .78 24 33 92 101 0 2679 2182 497 .878 1.139 -.188
5 5675 3288 5022 2622 653 666 null null 0 0 null null null .86 .84 24 33 102 111 0 2717 2166 551 .844 1.185 -.245
6 5716 3452 5038 2606 678 846 null null 0 0 null null null .76 .77 24 33 112 121 0 2852 2153 699 1.031 .97 .044
7 5433 3194 4896 2624 537 570 null null 0 0 null null null .74 .71 24 33 122 131 0 2639 2168 471 .877 1.14 -.189
8 5977 4143 5052 2664 925 1479 null null 0 0 null null null .7 .89 24 33 132 141 0 3423 2201 1222 1.321 .757 .402
9 5868 3636 5019 2640 849 996 null null 0 0 null null null .87 .9 24 33 142 151 0 3004 2181 823 .969 1.032 -.045
10 5840 3652 4936 2700 904 952 null null 0 0 null null null .98 .89 24 33 152 161 0 3018 2231 787 .871 1.149 -.2
11 5850 3665 4916 2615 934 1050 null null 0 0 null null null 1.01 .91 24 33 162 171 0 3028 2161 867 .928 1.077 -.107
12 5642 3451 4833 2632 809 819 null null 0 0 null null null .94 .86 25 34 172 181 0 2852 2175 677 .837 1.195 -.257
13 5159 2842 4754 2393 405 449 null null 0 0 null null null -.02 -.02 25 34 182 191 0 2348 1977 371 .916 1.092 -.127
14 5240 2996 4874 2632 366 364 null null 0 0 null null null .27 .24 25 34 192 201 0 2476 2175 301 .822 1.216 -.282
15 5221 2970 4758 2548 463 422 null null 0 0 null null null .28 .25 25 34 202 211 0 2454 2105 349 .754 1.327 -.408
16 5261 2869 4768 2353 493 516 null null 0 0 null null null .69 .66 25 34 212 221 0 2371 1944 427 .866 1.155 -.207
17 5318 3099 4736 2504 582 595 null null 0 0 null null null .79 .81 25 34 222 231 0 2561 2069 492 .845 1.183 -.242
18 5129 2845 4729 2362 400 483 null null 0 0 null null null .39 .39 25 34 232 241 0 2351 1952 399 .998 1.003 -.004
19 25551 2853 4918 2422 20633 431 null null 0 0 null null null 54.61 .61 25 34 242 251 0 2357 2001 356 .017 57.958 -5.857
20 5607 5809 4610 2300 997 3509 null null 0 0 null null null .12 .72 25 34 252 261 0 4800 1900 2900 2.909 .344 1.54

Total number of rows: 7680

Table truncated, full table size 892 Kbytes.




Supplementary data files not provided

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