I seem to be having some trouble generating an average file for a chip
effects set. I'm following the CRMA2 vignette (skipping the fragment
lengths normalisation). The CES seems to be generated OK, but
getAverage returns '0' for all values. Any ideas why? missing the frag-
length normalisation shouldn't affect this should it?
thanks
-s
> print(ces); print(ces[10000]);
CnChipEffectSet:
Name: AgSNP01_set
Tags: ACC,-XY,BPN,-XY,AVG,A+B
Path: plmData/AgSNP01_set,ACC,-XY,BPN,-XY,AVG,A+B/Ag_SNP_1m520721
Platform: Affymetrix
Chip type: Ag_SNP_1m520721,monocell
Number of arrays: 81
Names: EROSE_p_MS_Pop_Struct_Bamako_Ag_SNP_1m520721_A01_458244,
EROSE_p_MS_Pop_Struct_Bamako_Ag_SNP_1m520721_A02_458242, ...,
SAGAS_p_MS_Pop_Pilot1_MM4
g_SNP_1m520721_D08_445850
Time period: 2010-02-16 16:39:47 -- 2010-02-16 16:40:00
Total file size: 1240.10MB
RAM: 0.15MB
Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
combineAlleles: logi TRUE)
$Ag_2L_005857148
$Ag_2L_005857148$AT
$Ag_2L_005857148$AT$theta
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,
11] [,12]
[1,] 40607 49887 58641 74699 73849 59042 57730 44588 56064 53004 47275
43394
[,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,
23] [,24]
[1,] 48138 58073 41664 39946 24412 55460 49378 91170 60162 53812 38040
32548
[,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,
35] [,36]
[1,] 4639 6035 63732 62983 70399 8569 10699 56710 63548 40405 49868
33613
[,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,
47] [,48]
[1,] 44585 20986 33751 49092 43146 42322 38705 30467 31034 23933 54582
32668
[,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57] [,58] [,
59] [,60]
[1,] 28798 23453 65232 45382 65549 81326 172111 45896 33892 42695
61220 27770
[,61] [,62] [,63] [,64] [,65] [,66] [,67] [,68] [,69] [,70] [,
71] [,72]
[1,] 90138 36600 21338 30336 27390 37789 38993 33366 15584 2688 35110
36887
[,73] [,74] [,75] [,76] [,77] [,78] [,79] [,80] [,81]
[1,] 39633 37054 47837 47488 48989 36130 35849 20710 33560
> ceR <- getAverageFile(ces, verbose=verbose);
20100218 13:21:08|Retrieving average cell signals across 81 arrays...
CnChipEffectFile:
Name: .average-intensities-median-mad
Tags: f2e3009e11cbfd8257aa2ba6118e5039
Full name: .average-intensities-median-
mad,f2e3009e11cbfd8257aa2ba6118e5039
Pathname: plmData/AgSNP01_set,ACC,-XY,BPN,-XY,AVG,A+B/
Ag_SNP_1m520721/.average-intensities-median-
mad,f2e3009e11cbfd8257aa2ba6118e5039.CEL
File size: 15.31 MB (16053637 bytes)
RAM: 0.03 MB
File format: v4 (binary; XDA)
Platform: Affymetrix
Chip type: Ag_SNP_1m520721,monocell
Timestamp: 2010-02-16 16:41:57
Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
combineAlleles: logi TRUE)
20100218 13:21:09|Retrieving average cell signals across 81
arrays...done
> print(ceR); print(ceR[10000]);
CnChipEffectFile:
Name: .average-intensities-median-mad
Tags: f2e3009e11cbfd8257aa2ba6118e5039
Full name: .average-intensities-median-
mad,f2e3009e11cbfd8257aa2ba6118e5039
Pathname: plmData/AgSNP01_set,ACC,-XY,BPN,-XY,AVG,A+B/
Ag_SNP_1m520721/.average-intensities-median-
mad,f2e3009e11cbfd8257aa2ba6118e5039.CEL
File size: 15.31 MB (16053637 bytes)
RAM: 0.03 MB
File format: v4 (binary; XDA)
Platform: Affymetrix
Chip type: Ag_SNP_1m520721,monocell
Timestamp: 2010-02-16 16:41:57
Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
combineAlleles: logi TRUE)
$Ag_2L_005857148
$Ag_2L_005857148$AT
$Ag_2L_005857148$AT$theta
[1] 0
--
Seth Redmond
Scientific Programmer, VectorBase
Kafatos / Christophides Groups
Div. Cell and Molecular Biology
Imperial College, London
[email protected]
--
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