Hi Seth, On Thu, Feb 18, 2010 at 5:32 AM, seth redmond <seth.redm...@imperial.ac.uk> wrote: > 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?
No, it shouldn't. Can you post your entire script and your sessionInfo() ? Best, Pierre. > 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 > > seth.redm...@imperial.ac.uk > > -- > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe from this group, send email to > aroma-affymetrix-unsubscr...@googlegroups.com > For more options, visit this group at > http://groups.google.com/group/aroma-affymetrix?hl=en -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en
