Hello,

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

Command:

library(affy)

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

boxplot(raw)

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).

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 org.Mm.eg.db_3.0.0               
 [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            

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