invalid class NChannelSet object: featureNames differ between assayData and featureData
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Entering edit mode
4.2 years ago
thyleal ▴ 150

everyone.

I'm analyzing a two-channel microarray following an example from Bioconductor Case Studies book. I'm stuck in this error:

invalid class “NChannelSet” object: featureNames differ between assayData and featureData Does anyone know how to fix it?

The line that resulted in the error is:

assayData(NORM_dat) = assayDataNew(A=(r+g)/2, M=r-g)

Some info on my objects:

class(NORM_dat)
[1] "NChannelSet"
attr(,"package")
[1] "Biobase"

[1] "AnnotatedDataFrame"
attr(,"package")
[1] "Biobase"
Thank you so much!

Thyago

R session

R version 3.3.2 (2016-10-31)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Portuguese_Brazil.1252  LC_CTYPE=Portuguese_Brazil.1252   
[3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C                      
[5] LC_TIME=Portuguese_Brazil.1252    

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

other attached packages:
 [1] hexbin_1.27.1        vsn_3.42.3           geneplotter_1.52.0  
 [4] annotate_1.52.1      XML_3.98-1.5         AnnotationDbi_1.36.2
 [7] IRanges_2.8.1        S4Vectors_0.12.1     lattice_0.20-34     
[10] marray_1.52.0        limma_3.30.11        GEOquery_2.40.0     
[13] Biobase_2.34.0       BiocGenerics_0.20.0 

loaded via a namespace (and not attached):
 [1] RColorBrewer_1.1-2    preprocessCore_1.36.0 digest_0.6.12        
 [4] R6_2.2.0              scales_0.4.1          assertthat_0.1       
 [7] grid_3.3.2            bitops_1.0-6          httr_1.2.1           
[10] zlibbioc_1.20.0       RSQLite_1.1-2         munsell_0.4.3        
[13] tibble_1.2            affy_1.52.0           DBI_0.5-1            
[16] labeling_0.3          KernSmooth_2.23-15    ggplot2_2.2.1        
[19] BiocInstaller_1.24.0  plyr_1.8.4            gtable_0.2.0         
[22] colorspace_1.3-2      RCurl_1.95-4.8        tools_3.3.2          
[25] affyio_1.44.0         xtable_1.8-2          lazyeval_0.2.0       
[28] memoise_1.0.0         Rcpp_0.12.9          
>
Microarray bioconductor biobase NChannelSet • 1.8k views
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