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Sample GSM75971 Query DataSets for GSM75971
Status Public on Sep 24, 2005
Title DES459 (mec1-) + 0.02% MMS - 5 min
Sample type RNA
 
Channel 1
Source name time = 0 min
Organism Saccharomyces cerevisiae
Characteristics time = 0 min
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name time = 5 min
Organism Saccharomyces cerevisiae
Characteristics time = 5 min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: DNA damage, MMS
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/6362.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 Sep 23, 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 GPL51
Series (1)
GSE3358 DNA damage responses and Mec1p

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
1 293 117 49 18 244 99 53 21 88 89 .389 145 1206 .391 .79 106 121 189 204 0 114 17 97 .398 2.515 -1.331
2 213 197 48 17 165 180 51 19 44 53 .917 145 1049 1.096 .94 105 120 206 221 0 193 16 177 1.073 .932 .101
3 982 1089 45 16 937 1073 46 16 77 86 1.145 145 1058 1.045 .947 105 120 224 239 0 1067 15 1052 1.123 .891 .167
4 59 25 44 16 15 9 45 16 19 17 .429 145 1049 .566 .811 105 120 241 256 0 24 15 9 .6 1.667 -.737
5 495 515 43 16 452 499 44 16 75 82 1.12 145 1062 1.016 .929 105 120 259 274 0 504 15 489 1.082 .924 .114
6 47 19 43 16 4 3 44 16 15 16 .556 145 1049 .411 .576 105 120 277 292 0 18 15 3 .75 1.333 -.415
7 41 17 43 16 null 1 61 30 0 12 .778 145 1008 null null 105 120 294 309 0 16 15 1 null null null
8 75 107 42 16 33 91 60 30 28 40 2.769 145 1030 .711 .436 105 120 310 325 0 104 15 89 2.697 .371 1.431
9 44 18 44 16 null 2 61 29 6 16 .714 145 1054 .305 .262 105 120 328 343 0 17 15 2 null null null
10 43 14 44 16 null null 45 16 4 6 .471 145 1002 null null 105 120 346 361 0 13 15 null null null null
11 45 15 45 16 null null 45 15 4 4 .556 145 993 .02 .045 105 120 363 378 0 14 15 null null null null
12 44 16 44 15 null 1 44 15 4 16 .417 145 1032 .052 .087 105 120 381 396 0 15 14 1 null null null
13 40 15 43 16 null null 44 16 2 8 1 145 1017 .082 .139 105 120 399 414 0 14 15 null null null null
14 43 17 41 15 2 2 43 15 7 16 .417 145 1017 .091 .068 105 120 416 431 0 16 14 2 1 1 0
15 41 14 41 14 null null 42 15 6 12 .8 145 1040 .022 .043 105 120 434 449 0 13 13 null null null null
16 39 13 41 14 null null 42 14 4 4 .636 145 1017 .06 .143 105 120 452 467 0 12 13 null null null null
17 42 14 41 14 1 null 42 14 8 11 .276 145 1043 .043 .109 105 120 469 484 0 13 13 null null null null
18 41 14 41 14 null null 42 15 6 10 .5 145 1054 null null 105 120 489 504 0 13 13 null null null null
19 42 15 41 14 1 1 42 15 8 16 .5 145 994 null null 105 120 506 521 0 14 13 1 1 1 0
20 41 15 41 16 null null 42 15 4 11 .6 145 1038 null null 104 119 522 537 0 14 15 null null null null

Total number of rows: 9216

Table truncated, full table size 960 Kbytes.




Supplementary data files not provided
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