Question: Affe package mas5 error
0
gravatar for yuyingxie
11 months ago by
yuyingxie0
yuyingxie0 wrote:

 

Hi folks,

I am currently running affy to process some microarray data and got some error message when I called mas5

> cel = ReadAffy(cdfname="hgu133ahsentrezgcdf")

> e   = exprs(mas5(cel))

background correction: mas 

PM/MM correction : mas 

expression values: mas 

background correcting...Error in .validate_assayDataElementReplace(obj, value) : 

  object and replacement value have different dimensions

I have googled around but couldn't fix it. 

I also include the sessionInfo below. Thanks so mucn for your hel!

 

 

 sessionInfo()

R version 3.5.0 (2018-04-23)

Platform: x86_64-apple-darwin15.6.0 (64-bit)

Running under: macOS High Sierra 10.13.4

 

Matrix products: default

BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib

LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

 

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

 

attached base packages:

[1] parallel  stats4    stats     graphics  grDevices utils     datasets 

[8] methods   base     

 

other attached packages:

 [1] BiocInstaller_1.30.0       hgu133ahsentrezg.db_18.0.0

 [3] org.Hs.eg.db_3.6.0         hgu133ahsentrezgcdf_18.0.0

 [5] affy_1.58.0                preprocessCore_1.42.0     

 [7] annotate_1.58.0            XML_3.98-1.11             

 [9] AnnotationDbi_1.42.1       IRanges_2.14.10           

[11] S4Vectors_0.18.2           Biobase_2.40.0            

[13] BiocGenerics_0.26.0       

 

loaded via a namespace (and not attached):

 [1] Rcpp_0.12.17    zlibbioc_1.26.0 bit_1.1-13      xtable_1.8-2   

 [5] blob_1.1.1      tools_3.5.0     DBI_1.0.0       bit64_0.9-7    

 [9] digest_0.6.15   affyio_1.50.0   bitops_1.0-6    RCurl_1.95-4.10

[13] memoise_1.1.0   RSQLite_2.1.1   compiler_3.5.0  pkgconfig_2.0.1

 

affy affy mas5 • 247 views
ADD COMMENTlink written 11 months ago by yuyingxie0
1

It's working fine for me using some similar old (1st generation) mouse arrays that I had at hand.

However, I noticed that you are using version 18 of the custom CDF, which was released more than 4 years ago.... Maybe these old CDFs are not compatible anymore with the current version of R/BioC? The latest custom CDFs have version 22.

 

> affy.data <- ReadAffy(cdfname="moe430ammentrezg")
> head(exprs(mas5(affy.data)))
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...done.
12487 ids to be processed
|                    |
|####################|
             KOcontrol2.CEL KOcontrol3.CEL KOcontrol5.CEL  KOWY7.CEL KOWY8.CEL
100017_at         281.03718      300.30893     349.325229 492.731476 368.46865
100019_at         108.10902      155.00969      39.096128 168.429747 137.63542
100037258_at      364.01194      366.23043     377.799635 406.224641 422.37511
100038347_at      570.81180      561.18303     368.534263 409.663796 479.11048
100038746_at       12.95754       20.76136       5.290644   3.778448   2.74952
100040018_at      233.81823      308.00518     225.531818 326.181424 382.40645

 

> sessionInfo()
R version 3.5.0 Patched (2018-05-24 r74786)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] moe430ammentrezgcdf_22.0.0 AnnotationDbi_1.42.1      
 [3] IRanges_2.14.10            S4Vectors_0.18.2          
 [5] affyPLM_1.56.0             preprocessCore_1.42.0     
 [7] gcrma_2.52.0               affy_1.58.0               
 [9] Biobase_2.40.0             BiocGenerics_0.26.0       
[11] BiocInstaller_1.30.0      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17      Biostrings_2.48.0 digest_0.6.15     DBI_1.0.0        
 [5] RSQLite_2.1.1     zlibbioc_1.26.0   XVector_0.20.0    affyio_1.50.0    
 [9] blob_1.1.1        splines_3.5.0     tools_3.5.0       bit64_0.9-7      
[13] bit_1.1-13        compiler_3.5.0    memoise_1.1.0    
>

 

ADD REPLYlink written 11 months ago by Guido Hooiveld2.4k

Thanks for your help. I used another computer for the same code, and it worked. It is weird that it just didn't work on my Mac. 

ADD REPLYlink written 11 months ago by yuyingxie0
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