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Sample GSM38444 Query DataSets for GSM38444
Status Public on Sep 04, 2005
Title Muvar_21w54w
Sample type RNA
 
Channel 1
Source name Mutation accumulation line 21, start of pupariation (white prepupae)
Organism Drosophila melanogaster
Extracted molecule total RNA
 
Channel 2
Source name Mutation accumulation line 54, start of pupariation (white prepupae)
Organism Drosophila melanogaster
Extracted molecule total RNA
 
 
Description Comparison between mutation accumulation lines 21 at the start of pupariation (white prepupae) and 54 at the start of pupariation (white prepupae).
see D Houle and SV Nuzhdin. 2003. Genetical Research 83:7-18 for details of the lines.
Array images analyzed using Spot (CSIRO) v2.0. http://spot.cmis.csiro.au/spot/index.php
Sample_series_id: GSE2126
Keywords = evolution, quantitative genetics, mutation, Drosophila melanogaster
 
Submission date Jan 04, 2005
Last update date Aug 01, 2005
Contact name Scott A Rifkin
Phone 617-496-5540
URL http://kim.bio.upenn.edu/~scott/
Organization name Harvard University
Department OEB
Lab Hartl Lab
Street address 16 Divinity Ave
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
 
Platform ID GPL1779
Series (1)
GSE2126 Drosophila melanogaster mutation accumulation lines

Data table header descriptions
ID_REF
BLOCK block on the array (see platform description)
ROW row in the block (max = 25)
COLUMN column in the block (max = 25)
AREA The number of pixels in the segmented spot
CH1_MEAN The average pixel value within the spot for sample 1
CH1_MEDIAN The average pixel value within the spot for sample 1
CH1_IQR The interquartile range of the logged pixel values within the spot for sample 1
CH1_BGMEAN The average pixel value in the background region for sample 1
CH1_BGMEDIAN The median pixel value in the background region for sample 1
CH1_BGSD The interquartile range of the logged pixel values in the background region for sample 1
CH1_VALLEY Median of median image values in four neighbouring valley regions for sample 1: Valley regions are square regions between spots
CH1_MORPH Value of a morphological opening of sample 1 at the nominal spot centre. Openings and erosions use a rectangular structuring element with side lengths equal to twice the average horizontal and vertical distances between spots
CH1_MORPH_ERODE Value of a morphological erosion of sample 1 at the nominal spot centre
CH1_MORPH_CLOSE_OPEN Value of a morphological closing followed by a morphological opening of sample 1 at the nominal spot centre
CH1_TRANSFORMED Log-2 value for sample 1 for a spot after sample and series normalizations. This is the value used in the subsequent analyses
CH2_MEAN The average pixel value within the spot for sample 2
CH2_MEDIAN The average pixel value within the spot for sample 2
CH2_IQR The interquartile range of the logged pixel values within the spot for sample 2
CH2_BGMEAN The average pixel value in the background region for sample 2
CH2_BGMEDIAN The median pixel value in the background region for sample 2
CH2_BGSD The interquartile range of the logged pixel values in the background region for sample 2
CH2_VALLEY Median of median image values in four neighbouring valley regions for sample 2: Valley regions are square regions between spots
CH2_MORPH Value of a morphological opening of sample 2 at the nominal spot centre. Openings and erosions use a rectangular structuring element with side lengths equal to twice the average horizontal and vertical distances between spots
CH2_MORPH_ERODE Value of a morphological erosion of sample 2 at the nominal spot centre
CH2_MORPH_CLOSE_OPEN Value of a morphological closing followed by a morphological opening of sample 2 at the nominal spot centre
CH2_TRANSFORMED Log-2 value for sample 2 for a spot after sample and series normalizations. This is the value used in the subsequent analyses
VALUE The base-2 log of the background-adjusted ratio, R/G, using R/Gmedian for spot value and morphR/G for background. Note that this value is NOT used in the subsequent analyses (see CH1&CH2_TRANSFORMED)
PERIMETER The perimeter of the spot as measured by the number of pixels in the spot which have a neighbouring pixel outside the spot. Each pixel is considered to have 8 neighbours in this process
CIRCULARITY A measure of circularity of the spot equal to area</tt> times four pi divided by perimeter squared. This is ideally one for circles and more than one for other shapes
FLAG A flag which is one if the spot area is greater than the product of the horizontal and vertical average spot separations, or if the spot is flagged by visual inspection, or flagged in the platform

Data table
ID_REF BLOCK ROW COLUMN AREA CH1_MEAN CH1_MEDIAN CH1_IQR CH1_BGMEAN CH1_BGMEDIAN CH1_BGSD CH1_VALLEY CH1_MORPH CH1_MORPH_ERODE CH1_MORPH_CLOSE_OPEN CH1_TRANSFORMED CH2_MEAN CH2_MEDIAN CH2_IQR CH2_BGMEAN CH2_BGMEDIAN CH2_BGSD CH2_VALLEY CH2_MORPH CH2_MORPH_ERODE CH2_MORPH_CLOSE_OPEN CH2_TRANSFORMED VALUE PERIMETER CIRCULARITY FLAG
0 1 1 1 27 249.037037037037 183 1.07938092674022 110.75 93 0.476924072090309 76 34 32 78 11.9283852247 144.407407407407 109 1.04145387482816 90.4351851851852 78 0.658661004488776 84 14 10 83 11.7701929549 -0.649312912131214 20 0.848230016469244 1
1 1 1 2 22 271.454545454545 175 1.32980417316515 107.1875 91 0.436102077570054 80 41 33 80 11.8910904686 167.5 122 1.23474446299269 87.34375 77 0.585901650206347 81 13 10 83 11.8185118305 -0.297904865680846 16 1.07992247467149 1
2 1 1 3 28 201.321428571429 127 0.770336819251075 113.561403508772 89 0.410020924644026 80 41 34 80 11.7352098787 136.178571428571 94 0.749500117111077 94.5438596491228 84 0.693147180559945 80 13 10 83 11.7141566308 -0.0864147518174721 20 0.879645943005142 1
3 1 1 4 23 215.173913043478 132 1.18029031968238 110.441176470588 96 0.51345374617226 80 41 28 80 11.7550730255 156.826086956522 93 1.15418213982292 87.6960784313726 78 0.475845904869964 80 13 5 79 11.7097903118 -0.185866545311334 17 1.00009177899744 1
4 1 1 5 21 325.142857142857 156 1.70049095511511 101.03125 87 0.46813621507094 84 39 28 75 11.843406066 191.809523809524 126 1.09527338740260 86.7916666666667 75 0.6176396280518 80 10 1 77 11.8403890161 -0.0123837244558329 16 1.03083508945915 1
5 1 1 6 29 244.862068965517 164 1.08674271311273 159.561403508772 98 0.559615787935423 84 38 28 85 11.8694538443 149.620689655172 101 0.913620503318277 116.157894736842 88 0.651300070624445 87 10 1 79 11.7550730255 -0.469485283301221 20 0.91106186954104 1
6 1 1 7 43 160.279069767442 102 0.331645195872897 148.884057971014 88 0.497032301633655 81 38 28 86 11.6313588882 123.116279069767 99 0.586284035017584 102.557971014493 81 0.63304325649024 89 10 7 80 11.7472619449 0.475733430966398 28 0.689226959716128 1
7 1 1 8 21 494.47619047619 381 2.05945139680333 130.625 104 0.522801814812706 81 43 28 86 12.2162857554 357.904761904762 278 1.72822144842407 97.1875 87 0.574430873720564 89 14 7 85 12.1294351471 -0.356485316923731 16 1.03083508945915 1
8 1 1 9 23 285.173913043478 138 1.32306217589637 103.019607843137 95 0.376235469793226 84 43 30 86 11.7701929549 154.478260869565 126 0.836659462182148 88.1372549019608 83 0.535142931416697 87 14 14 85 11.8280549731 0.237499313726656 17 1.00009177899744 1
9 1 1 10 69 175.014492753623 105 0.448693842658984 124.897849462366 88 0.410020924644026 84 43 31 84 11.6201997237 125.666666666667 96 0.599328425342291 104.295698924731 89 0.70158604920581 87 14 14 85 11.718469374 0.403355694231209 46 0.40977295481606 1
10 1 1 11 22 626.363636363636 479 1.73285919812833 111.274509803922 95 0.42744401482694 81 37 28 81 12.3105762973 467.227272727273 433 1.64222773525709 99.6274509803922 91 0.767870726755882 83 14 0 85 12.2917933486 -0.07709612569208 17 0.956609527736684 1
11 1 1 12 21 290.095238095238 132 2.00115432035054 137.166666666667 87 0.419070760163943 84 38 28 84 11.7664735111 217.714285714286 116 1.47048645234024 115.46875 91 0.66865616055165 76 13 0 88 11.7986111861 0.131911675505581 16 1.03083508945915 1
12 1 1 13 22 408.272727272727 315 1.81117755508516 122.862745098039 100 0.525531771155686 87 38 28 85 12.1463304293 272.545454545455 174 1.31998436033394 142.754901960784 103 0.7339691750802 79 13 6 92 11.9556105055 -0.782825287934571 17 0.956609527736684 1
13 1 1 14 27 264.777777777778 133 1.10465460312407 114.972222222222 99 0.430157720698536 97 38 33 85 11.7701929549 165.888888888889 115 1.34883679858499 92.9907407407407 81 0.591364486250002 105 16 6 92 11.7846892015 0.0595010117486617 20 0.848230016469244 1
14 1 1 15 21 314.285714285714 120 1.70739243049152 130.020833333333 102 0.529079064075341 91 43 33 88 11.6963561609 226.952380952381 72 2.01728114294723 88.2604166666667 79 0.628608659422373 83 16 9 79 11.5844247189 -0.459431618637297 16 1.03083508945915 1
15 1 1 16 21 380.904761904762 217 1.34010497865052 120.125 102 0.41744129915488 91 43 39 88 11.9829035788 240.476190476190 129 1.04145387482816 90.9791666666667 78 0.583947888594953 78 20 9 86 11.8185118305 -0.674759171071802 16 1.03083508945915 1
16 1 1 17 24 520.041666666667 493 0.914919929740377 147.009803921569 101 0.563094052311747 88 43 39 88 12.3168811149 266.416666666667 249 1.16586451567728 111.450980392157 81 0.600253433667249 75 20 9 86 12.0794445745 -0.974577403120093 18 0.93084226773031 1
17 1 1 18 22 376.363636363636 215 1.47478102728784 116.019607843137 100 0.401440957808439 92 48 39 95 11.9684711166 355.272727272727 129 1.73321601361544 104.941176470588 88 0.483174092435481 82 20 9 85 11.8185118305 -0.615519967697127 17 0.956609527736684 1
18 1 1 19 21 404.857142857143 128 0.969400557188103 143.197916666667 98 0.41376391092286 95 48 38 96 11.7097903118 220.666666666667 93 0.986249320481065 120.447916666667 88 0.727048732235627 82 18 9 94 11.6871060439 -0.0931094043914813 16 1.03083508945915 1
19 1 1 20 41 112.780487804878 97 0.555946059046461 109.947368421053 101 0.388657989791784 97 48 38 96 11.5374905496 99.609756097561 94 0.565633860260986 93.6992481203008 90 0.617797743318159 91 18 7 94 11.6917615313 0.633217669328378 29 0.612629245170899 1

Total number of rows: 20000

Table truncated, full table size 5109 Kbytes.




Supplementary data files not provided
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