Question: Mouse Transcriptome Assay 1.0 processing and annotation
gravatar for alakatos
4.7 years ago by
United States
alakatos110 wrote:


I processed my GeneChip® Mouse Transcriptome Assay 1.0 (MTA10) arrays.



raw <- ReadAffy(cdfname = "mta10.r1.genecdf", phenoData="phenotype.txt")


Warning message: In data.row.names(row.names, rowsi, i) : some row.names duplicated: 16,17,18,23,24,25,26,27,28,29,31,33,34,35,36,38,42,43,44,45,47,49,50,51,54,55,56,62,64,66,67,69,70,71,73,74,76,81,82,83,85,87,88,89,91,92,94,96,97,98,99,101,102,105,108,109,112,115,117,118,119,121,124,125,127,128,129,131,132,133,134,135,137,138,139,140,142,144,145,146,147,151,152,153,154,155,156,159,161,162,166,169,176,180,181,183,186,190,191,192,193,194,195,197,198,203,208,211,212,213,215,220,222,223,224,226,228,229,232,233,236,238,241,242,244,245,246,247,248,251,254,255,257,261,262,266,267,270,273,274,275,276,278,280,284,286,287,288,293,294,295,297,298,299,302,308,309,312,314,316,318,321,323,326,327,328,330,331,333,336,338,339,340,341,344,346,349,354,356,357,359,360,361,362,364,365,366,368,370,374,379,380,381,382,383,386,387,391,392,393,396,398,399,400,403,404,405,409,410,413,415,416,420,422,424,425,426,428,429,430,434,435,436,439,440,441,442,443,444,446,447,450,452,453,454,458,460,461,464,465,466,467,470,475,478,480,482,484,486,487,490,491,493,494,495,498, [... truncated]

eset = rma(raw, target="core")
annotation(eset) <- "mta10sttranscriptcluster.db"

              0215F-02_01-(MTA-1_0).CEL        0215F-02_02-(MTA-1_0).CEL      etc    
20550008              5.609107                                    5.647651
20550009              6.488896                                    6.488896
20550010              6.284914                                    6.284914
20550011              6.738269                                    6.738269
20550012              6.668315                                    6.668315 

In addition, the same files were processed  in Affy Expression Console (SST-RMA).

When I compared the 2 results,  the boxplots  (Expression console (Q1 ~ 4.2; median ~6; Q3~ 8), R(affy)(Q1 ~ 6.25; median ~6.6; Q3~ 7).


I am wondering  if I used the correct  tool ("affy") for  this type of array?

 Is there any better tool(s)  (e.g. "puma") or recommendation for this array ?



Thank you for your help in advance.



R version 3.1.2 (2014-10-31)

Platform: x86_64-w64-mingw32/x64 (64-bit)

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] oligo_1.30.0                      Biostrings_2.34.1                 XVector_0.6.0                    
 [4] oligoClasses_1.28.0               mta10sttranscriptcluster.db_8.2.0               
 [7] mta10.r1.genecdf_1.42.0           affy_1.44.0                       biomaRt_2.22.0                   
[10] gplots_2.16.0                     ggplot2_1.0.0                     GGally_0.5.0                     
[13] hwriter_1.3.2                     ReportingTools_2.6.0              RSQLite_1.0.0                    
[16] DBI_0.3.1                         knitr_1.9                         limma_3.22.6                     
[19] annotate_1.44.0                   XML_3.98-1.1                      AnnotationDbi_1.28.1             
[22] GenomeInfoDb_1.2.4                IRanges_2.0.1                     S4Vectors_0.4.0                  
[25] genefilter_1.48.1                 Biobase_2.26.0                    BiocGenerics_0.12.1              
[28] RColorBrewer_1.1-2            




ADD COMMENTlink modified 4.2 years ago by jacorvar40 • written 4.7 years ago by alakatos110
Answer: Mouse Transcriptome Assay 1.0 processing and annotation
gravatar for jacorvar
4.2 years ago by
European Union
jacorvar40 wrote:

Did you try to read the CEL files with oligo package instead of Affy?

ADD COMMENTlink written 4.2 years ago by jacorvar40
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 365 users visited in the last hour