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Sample GSM71626 Query DataSets for GSM71626
Status Public on Aug 24, 2005
Title cell cycle-alpha factor, fkh1, fkh2 030min
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 030 min
Organism Saccharomyces cerevisiae
Characteristics 030 min
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Cell-cycle, Forkheads
Image: http://smd.stanford.edu/MicroArray/gifs/1999-12/485.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
1 271 323 56 63 215 260 60 67 62 67 1.183 177 1119 .962 .85 105 120 105 120 0 414 81 333 1.549 .646 .631
2 98 100 54 63 44 37 58 67 36 34 1.19 177 892 .402 .722 105 120 122 137 0 128 81 47 1.068 .936 .095
3 656 551 53 60 603 491 57 63 64 58 .866 177 918 .764 .917 105 120 139 154 0 706 77 629 1.043 .959 .061
4 144 134 55 60 89 74 59 63 45 31 .736 177 928 .766 .867 105 120 157 172 0 172 77 95 1.067 .937 .094
5 364 306 54 62 310 244 58 65 54 50 .857 177 928 .742 .925 105 120 174 189 0 392 79 313 1.01 .99 .014
6 306 224 52 64 254 160 57 67 41 24 .587 177 928 .651 .92 105 120 192 207 0 287 82 205 .807 1.239 -.309
7 49 57 52 63 null null 56 65 18 6 .786 177 928 -.031 -.04 105 120 209 224 0 73 81 null null null null
8 57 56 49 61 8 null 55 62 31 7 .429 177 928 -.001 -.002 105 120 227 242 0 72 78 null null null null
9 53 65 48 58 5 7 54 61 28 20 .714 177 928 -.024 -.039 105 120 244 259 0 83 74 9 1.8 .556 .848
10 60 64 50 58 10 6 54 60 26 17 .75 177 919 .259 .479 105 120 262 277 0 82 74 8 .8 1.25 -.322
11 59 63 51 59 8 4 55 61 24 12 .563 177 928 .127 .155 105 120 279 294 0 81 76 5 .625 1.6 -.678
12 52 63 50 60 2 3 55 63 20 15 .576 177 928 -.021 -.028 105 120 297 312 0 81 77 4 2 .5 1
13 58 65 50 62 8 3 56 64 28 14 .727 177 928 .013 .016 105 120 314 329 0 83 79 4 .5 2 -1
14 53 70 49 62 4 8 55 64 24 20 1 177 928 .056 .061 105 120 332 347 0 90 79 11 2.75 .364 1.459
15 57 64 49 62 8 2 54 64 31 17 .868 177 928 .024 .029 105 120 349 364 0 82 79 3 .375 2.667 -1.415
16 54 66 52 63 2 3 57 68 20 14 .768 177 928 .087 .104 105 120 367 382 0 85 81 4 2 .5 1
17 54 65 52 64 2 1 58 68 23 10 .541 177 928 .035 .052 105 120 384 399 0 83 82 1 .5 2 -1
18 59 66 54 64 5 2 58 69 28 15 .825 177 928 .046 .057 105 120 402 417 0 85 82 3 .6 1.667 -.737
19 60 67 53 64 7 3 56 69 26 14 1.039 177 928 .113 .148 105 120 419 434 0 86 82 4 .571 1.75 -.807
20 53 66 51 65 2 1 57 70 22 12 .862 177 928 .081 .108 105 120 437 452 0 85 83 2 1 1 0

Total number of rows: 9216

Table truncated, full table size 973 Kbytes.




Supplementary data files not provided
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