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Sample GSM75981 Query DataSets for GSM75981
Status Public on Sep 24, 2005
Title DES459 (mec1-) + 0.02% MMS - 60 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 = 60 min
Organism Saccharomyces cerevisiae
Characteristics time = 60 min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: DNA damage, MMS
Image: http://smd.stanford.edu/MicroArray/gifs/1999-10/8523.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 GPL2650
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
1 103 26 60 10 43 16 62 12 48 40 .48 193 1077 .41 .72 107 124 63 80 0 34 13 21 .488 2.048 -1.034
2 537 434 59 10 478 424 72 14 42 68 1.22 193 877 .62 .93 106 123 80 97 0 571 13 558 1.167 .857 .223
3 94 51 58 10 36 41 70 14 21 38 .88 193 866 .82 .88 106 123 98 115 0 67 13 54 1.5 .667 .585
4 859 745 58 11 801 734 60 13 42 62 1.07 193 852 .64 .93 106 123 115 132 0 980 14 966 1.206 .829 .27
5 2726 2416 58 12 2668 2404 65 15 89 92 1.16 193 867 .69 .94 106 123 133 150 0 3178 15 3163 1.186 .844 .246
6 374 229 60 12 314 217 67 15 36 57 .92 193 841 .45 .88 106 123 151 168 0 301 15 286 .911 1.098 -.135
7 56 12 60 12 -4 null 64 14 5 21 .51 193 877 .07 .21 105 122 168 185 0 15 15 null null null null
8 66 14 60 12 6 2 66 16 16 28 .66 193 877 .02 .06 105 122 186 203 0 18 15 3 .5 2 -1
9 62 14 60 11 2 3 65 15 12 32 .44 193 867 .1 .33 105 122 203 220 0 18 14 4 2 .5 1
10 61 13 60 10 1 3 66 16 9 31 .51 193 877 .04 .1 105 122 221 238 0 17 13 4 4 .25 2
11 60 12 60 10 null 2 69 16 8 31 .59 193 841 .02 .06 105 122 239 256 0 15 13 2 null null null
12 58 11 60 11 -2 null 68 18 7 24 .44 193 877 0 0 104 121 256 273 0 14 14 null null null null
13 66 12 62 11 4 1 70 19 13 24 .66 193 877 .08 .21 104 121 274 291 0 15 14 1 .25 4 -2
14 60 11 61 10 -1 1 69 18 9 26 .55 193 867 .01 .02 104 121 291 308 0 14 13 1 null null null
15 59 9 58 9 1 null 65 15 10 26 .5 193 877 .01 .05 104 121 309 326 0 11 11 null null null null
16 57 8 58 9 -1 -1 62 14 8 17 .6 193 841 .02 .09 104 121 327 344 0 10 11 -1 null null null
17 69 19 58 10 11 9 63 15 21 30 .75 193 877 .37 .62 103 120 344 361 0 25 13 12 1.091 .917 .126
18 61 14 64 12 -3 2 76 16 8 26 1.08 193 887 .11 .24 103 120 362 379 0 18 15 3 null null null
19 64 12 65 12 -1 null 76 14 7 19 .59 193 867 .05 .18 103 120 379 396 0 15 15 null null null null
20 62 12 66 12 -4 null 74 15 7 22 .46 193 867 .03 .12 103 120 397 414 0 15 15 null null null null

Total number of rows: 9216

Table truncated, full table size 958 Kbytes.




Supplementary data files not provided
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