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Experiment and Hybridizations Summary



Experiments:        

Please choose Species/Platform/Experiment
 

Experiment Submitter: caldo
Experiment Name: Cross-species Detection in Barley1 GeneChip Array
 

Experiment Visualization:     


Boxplots, Histogram and RNA Degeneration Curve:
  1. Boxplot of raw Perfect match(PM) probe intensities: The raw PM intensity change in distribution for different hybridizations.
  2. Boxplot of RMA expression values (log2-scale): The distribution of RMA expression values for different hybridizations.
  3. Boxplot of Affymetrix MAS5.0 expression (log2-scale): The distribution of Affymetrix MAS5.0 expression values for different hybridizations.
  4. Histogram of raw PM intensities: The raw PM intensity change in distribution for different hybridizations.
  5. RNA digestion plot: The raw PM intensity change with regard to probe pairs from 5' to 3'.

*Visualize  hybridizations by scatter plots and MVA plots
Check table below for more details on hybridizations. Click a hybridization link for their Full Details 


Information of Hybridizations from BB1 

HybridizationTREPFactor 1:
species
File_NameSample_ID & NameDownload Individual Data File
1 BB1_H111Barley0308-6BB1_S1
Expt# 11666-10
CEL
CHP
DAT
EXP
2 BB1_H212Barley0315-6BB1_S2
Expt # 11771-6
CEL
CHP
DAT
EXP
3 BB1_H321Wheat0308-1BB1_S3
Expt# 11666-1
CEL
CHP
DAT
EXP
4 BB1_H422Wheat0315-5BB1_S4
Expt# 11771-5
CEL
CHP
DAT
EXP
5 BB1_H531Oat0308-5BB1_S5
Expt# 11666-8
CEL
CHP
DAT
EXP
6 BB1_H632Oat0315-4BB1_S6
Expt# 11771-4
CEL
CHP
DAT
EXP
7 BB1_H741Sorghum0308-3BB1_S7
Expt# 11666-5
CEL
CHP
DAT
EXP
8 BB1_H842Sorghum0315-2BB1_S8
Expt # 11771-2
CEL
CHP
DAT
EXP
9 BB1_H951Corn0308-4BB1_S9
Expt# 11666-7
CEL
CHP
DAT
EXP
10 BB1_H1052Corn0315-3BB1_S10
Expt# 11771-3
CEL
CHP
DAT
EXP
11 BB1_H1161Rice0308-2BB1_S11
Expt# 11666-2
CEL
CHP
DAT
EXP
12 BB1_H1262Rice0315-1BB1_S12
Expt # 11771-1
CEL
CHP
DAT
EXP
T= Treatment; REP = Replicate


Expression Summary Statistic by Hybridization:
HybridizationTREPMin.1st Qu.MedianMean3rd Qu.Max
1 BB1_H111 9.506e-02
3.627
5.480e+01
5.220
1.797e+02
6.308
7.894e+02
6.631
5.172e+02
7.709
4.233e+04
14.310
2 BB1_H212 0.021
3.585
57.490
5.145
181.300
6.206
735.600
6.575
525.600
7.679
35530.000
14.300
3 BB1_H321 1.154e-01
2.409
2.503e+01
4.883
8.553e+01
5.918
3.293e+02
5.931
2.048e+02
6.844
3.661e+04
14.190
4 BB1_H422 1.591e-01
2.404
2.057e+01
4.867
6.919e+01
5.900
2.760e+02
5.933
1.640e+02
6.843
3.678e+04
14.170
5 BB1_H531 6.226e-02
2.342
1.874e+01
4.680
6.161e+01
5.681
1.388e+02
5.608
1.348e+02
6.498
2.577e+04
13.440
6 BB1_H632 0.184
2.411
14.680
4.680
48.890
5.682
129.800
5.607
113.500
6.498
26680.000
13.390
7 BB1_H741 8.607e-02
2.754
1.801e+01
4.750
5.697e+01
5.755
1.253e+02
5.717
1.336e+02
6.620
3.414e+04
13.460
8 BB1_H842 1.332e-01
2.730
1.643e+01
4.719
4.995e+01
5.734
1.154e+02
5.699
1.166e+02
6.603
3.246e+04
13.370
9 BB1_H951 0.117
3.885
21.080
5.415
68.440
6.052
148.600
6.107
161.700
6.690
35460.000
13.660
10 BB1_H1052 1.425e-01
3.826
3.357e+01
5.336
7.442e+01
5.954
1.470e+02
6.020
1.624e+02
6.577
2.654e+04
13.830
11 BB1_H1161 2.038e-01
2.303
1.714e+01
4.319
5.437e+01
5.282
1.113e+02
5.254
1.210e+02
6.141
3.276e+04
13.400
12 BB1_H1262 6.724e-02
2.259
1.102e+01
4.313
3.453e+01
5.276
8.488e+01
5.251
7.812e+01
6.142
3.102e+04
13.830
T= Treatment; REP = Replicate;
For each cell of statistic, upper row (red) is for MAS 5.0 and lower row (blue) is for RMA estimation.

 

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