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Sample GSM71621 Query DataSets for GSM71621
Status Public on Aug 24, 2005
Title cell cycle-alpha factor, fkh1, fkh2 060min
Sample type RNA
 
Channel 1
Source name Reference Pool
Organism Saccharomyces cerevisiae
Characteristics Reference Pool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 060 min
Organism Saccharomyces cerevisiae
Characteristics 060 min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/483.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 Aug 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)
GSE3182 Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth

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
1 231 314 55 43 176 271 63 48 71 78 1.525 177 1119 1.091 .82 125 140 29 44 0 327 45 282 1.602 .624 .68
2 103 87 55 43 48 44 63 48 43 40 .739 177 915 .771 .754 124 139 46 61 0 91 45 46 .958 1.043 -.061
3 440 517 55 43 385 474 65 49 70 65 1.125 177 928 1.111 .872 124 139 63 78 0 539 45 494 1.283 .779 .36
4 117 97 53 41 64 56 63 44 45 37 .581 177 928 .864 .823 124 139 81 96 0 101 43 58 .906 1.103 -.142
5 188 204 53 42 135 162 62 49 48 50 1.049 177 928 1.134 .925 124 139 98 113 0 213 44 169 1.252 .799 .324
6 74 62 52 43 22 19 60 50 38 27 .807 177 928 .479 .483 124 139 116 131 0 65 45 20 .909 1.1 -.138
7 65 46 53 43 12 3 61 49 28 16 .441 177 919 .165 .313 124 139 133 148 0 48 45 3 .25 4 -2
8 55 42 53 43 2 null 62 46 23 12 .667 177 906 .052 .097 124 139 151 166 0 44 45 null null null null
9 49 42 54 42 null null 64 45 16 12 .455 177 896 .129 .266 124 139 168 183 0 44 44 null null null null
10 57 48 51 41 6 7 61 43 24 22 .552 177 896 .121 .203 124 139 186 201 0 50 43 7 1.167 .857 .222
11 57 42 49 41 8 1 58 42 22 12 .792 177 896 .216 .395 124 139 203 218 0 44 43 1 .125 8 -3
12 67 44 51 41 16 3 66 47 25 18 .429 177 896 .087 .259 124 139 221 236 0 46 43 3 .188 5.333 -2.415
13 52 42 53 40 null 2 64 46 22 16 .444 177 896 .045 .086 124 139 238 253 0 44 42 2 null null null
14 55 41 49 39 6 2 83 48 27 16 .474 177 928 .078 .16 123 138 256 271 0 43 41 2 .333 3 -1.585
15 78 54 46 39 32 15 83 49 35 14 .469 177 928 .529 .903 123 138 273 288 0 56 41 15 .469 2.133 -1.093
16 61 45 47 39 14 6 89 47 33 21 .4 177 919 .259 .413 123 138 291 306 0 47 41 6 .429 2.333 -1.222
17 53 41 49 40 4 1 73 46 29 12 .347 177 928 .048 .106 123 138 308 323 0 43 42 1 .25 4 -2
18 53 40 50 39 3 1 61 42 24 16 .737 177 928 .004 .007 123 138 326 341 0 42 41 1 .333 3 -1.585
19 56 44 47 39 9 5 55 42 27 21 .447 177 919 .07 .159 123 138 343 358 0 46 41 5 .556 1.8 -.848
20 50 38 47 41 3 null 55 44 25 11 .4 177 905 -.026 -.048 123 138 361 376 0 40 43 null null null null

Total number of rows: 9216

Table truncated, full table size 979 Kbytes.




Supplementary data files not provided
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