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Sample GSM71657 Query DataSets for GSM71657
Status Public on Aug 25, 2005
Title Bladder_BW3vsC0
Sample type RNA
 
Channel 1
Source name C0
Organism Homo sapiens
Characteristics Normal urothelium pool (4 males)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name BW3
Organism Homo sapiens
Characteristics Individual tumoral bladder washing (pT2 G3)
Extracted molecule total RNA
Label Cy5
 
 
Description Bladder washing RNA degradation state 3.
filters to remove bad spots:
circularity>=0.4
area>=40
bg[RG]med/morph[RG]<=8
[RG]median/bg[RG]SD<=0.0045
badspot=0
Data processing log2((Rmedian-morphR)/(Gmedian-morphG)) adjusting previously mean intensity to 400 for all arrays and channels
 
Submission date Aug 23, 2005
Last update date Aug 24, 2005
Contact name Moises Burset Albareda
E-mail(s) [email protected]
Organization name Fundacio Puigvert
Department Molecular biology
Street address Cartagena, 340-350
City Barcelona
State/province Barcelona
ZIP/Postal code 08025
Country Spain
 
Platform ID GPL2767
Series (1)
GSE3192 Partially degraded RNA from bladder washing is a suitable sample for studying gene expression profiles of bladder cancer

Data table header descriptions
ID_REF
grid.r grid row
grid.c grid column
spot.r spot row in every grid
spot.c spot column in every grid
area number of pixels
Gmean pixels mean intensity (green)
Gmedian pixels median intensity (green)
GIQR inter quartile range (green) (dispersion of 50% of pixels closer to median)
Rmean pixels mean intensity (red)
Rmedian pixels median intensity (red)
RIQR inter quartile range (red) (dispersion of 50% of pixels closer to median)
bgGmean mean background intensity (green)
bgGmed median background intensity (green)
bgGSD background standard deviation (green)
bgRmean mean background intensity (red)
bgRmed median background intensity (red)
bgRSD background standard deviation (red)
valleyG mean of the background median for 4 diamond areas around the spot (green) (spot program for details)
valleyR mean of the background median for 4 diamond areas around the spot (red) (spot program for details)
morphG background estimation using morphological opening (green) (spot program for details)
morphG.erode background estimation using morphological erosion (green) (spot program for details)
morphG.close.open background estimation using morphological closing-opening (green) (spot program for details)
morphR background estimation using morphological opening (red) (spot program for details)
morphR.erode background estimation using morphological erosion (red) (spot program for details)
morphR.close.open background estimation using morphological closing-opening (red) (spot program for details)
logratio log2((Rmedian-morphR)/(Gmedian-morphG))
perimeter 2*sqrt(pi*area/circularity)
circularity 4*pi*area/perimeter^2
badspot if 0 -> good spot
nominal.center.row nominal center row
nominal.center.col nominal center column
VALUE final filtered and normalized log2ratio

Data table
ID_REF grid.r grid.c spot.r spot.c area Gmean Gmedian GIQR Rmean Rmedian RIQR bgGmean bgGmed bgGSD bgRmean bgRmed bgRSD valleyG valleyR morphG morphG.erode morphG.close.open morphR morphR.erode morphR.close.open logratio perimeter circularity badspot nominal.center.row nominal.center.col VALUE
0 1 1 1 1 91 2300.32 2444 0.330352 8668.07 9066 0.355411 241.278 172 0.30573 244.019 100 0.405465 157 89 110 100 157 56 54 89 1.94872 38 0.791925 0 108.826 104.913 1.99035
1 1 1 1 2 98 2421.18 2603 0.159001 8960.91 9595 0.179836 225.804 159 0.536578 348.554 99 1.44424 148 88 100 100 146 56 53 87 1.93018 40 0.76969 0 108.826 122.913 1.98139
2 1 1 1 3 58 232.724 193 0.221959 116.138 109 0.207014 142.552 138 0.150823 86.0276 86 0.16508 138 88 100 82 140 56 49 86 -0.811238 32 0.711767 0 108.826 141.913 -0.333424
3 1 1 1 4 11 344.818 240 0.639955 178.636 149 0.289729 175.738 169 0.35595 111.286 107 0.273538 136 85 97 82 133 56 49 85 -0.620713 10 1.3823 0 108.826 158.913 null
4 1 1 1 5 96 163.562 150 0.188256 97.1354 92 0.167992 138.103 136 0.175633 84.1959 82 0.193371 140 83 94 90 136 56 55 83 -0.63743 54 0.413708 0 108.826 176.913 null
5 1 1 1 6 61 170.098 163 0.180126 97.5902 95 0.218482 152.97 137 0.16525 89.0723 87 0.220543 147 86 97 90 136 58 53 85 -0.834941 40 0.479093 0 108.826 194.913 -0.0931094
6 1 1 1 7 81 18454.9 20467 0.250518 13501.5 14436 0.306848 812.237 189 1.6134 449.833 100 1.65658 152 87 100 90 136 58 53 85 -0.50237 36 0.785398 0 108.826 212.913 -0.404903
7 1 1 1 8 99 15970.1 15847 0.405207 11816.4 12026 0.370228 689.44 199 1.63629 399.988 109 1.63792 142 87 100 92 136 58 53 85 -0.395895 40 0.777544 0 108.826 230.913 -0.299275
8 1 1 1 9 9 2932.78 803 2.22327 202.111 128 0.612726 189.389 171 0.304321 123 117 0.263111 142 87 92 92 135 57 54 82 -3.32396 8 1.76715 0 108.826 248.913 null
9 1 1 1 10 9 5146.33 3387 2.45453 253.222 156 0.794168 215.625 184 0.477144 132.472 117 0.402092 137 86 95 92 135 59 56 80 -5.08484 8 1.76715 0 108.826 266.913 null
10 1 1 1 11 9 282.333 209 0.415617 118.778 106 0.320472 145.403 144 0.221592 87.2222 85 0.139762 148 86 96 92 135 59 56 83 -1.26559 8 1.76715 0 108.826 285.913 null
11 1 1 1 12 44 172.364 168 0.208467 97.2045 96 0.125163 138.167 138 0.138402 84.2407 82 0.156004 148 86 96 93 137 59 55 83 -0.960472 33 0.507732 0 108.826 302.913 -0.128733
12 1 1 1 13 50 149.32 147 0.154151 93.8 93 0.172469 134.503 133 0.157629 83.6228 83 0.157903 145 86 96 85 137 56 54 83 -0.462972 37 0.458962 0 108.826 322.913 null
13 1 1 1 14 12 235 213 0.529919 109.833 102 0.208297 146.678 145 0.173444 85.7556 87 0.173847 155 88 93 85 137 56 54 81 -1.38333 11 1.24625 0 108.826 339.913 null
14 1 1 1 15 9 334.111 202 0.839504 154.778 96 0.218254 146.236 142 0.255679 87.5833 88 0.184429 155 86 93 84 137 56 53 81 -1.44626 8 1.76715 0 108.826 357.913 null
15 1 1 1 16 77 151.234 145 0.184825 89.1039 89 0.136576 133.286 129 0.152969 83.4184 81 0.159849 132 84 93 84 129 56 53 81 -0.656046 53 0.344468 0 108.826 374.913 null
16 1 1 1 17 119 2435.84 2283 0.26928 748.639 717 0.24978 176.35 135 0.239404 89.5278 81 0.171148 127 83 94 84 127 54 50 81 -1.72319 44 0.772416 0 108.826 393.913 -1.57342
17 1 1 1 18 125 2380.94 2221 0.263696 751.84 716 0.268081 250.356 137 0.301924 117.372 84 0.212561 126 78 96 89 128 54 50 81 -1.68256 44 0.811362 0 108.826 411.913 -1.53552
18 1 1 1 19 108 1006.31 994 0.182505 1395.38 1383 0.208386 162.506 133 0.219859 109.635 84 0.228259 130 79 96 89 128 54 52 82 0.565554 42 0.76937 0 108.826 428.913 0.575074
19 1 1 1 20 123 964.699 1002 0.128728 1382.11 1439 0.190282 158.674 136 0.223144 105.696 85 0.223144 131 80 96 75 128 54 52 82 0.612303 46 0.730465 0 108.826 446.913 0.622149

Total number of rows: 27648

Table truncated, full table size 4667 Kbytes.




Supplementary data files not provided

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