rice affymetrix qc() function
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@zhangjianhai-12955
Last seen 4.2 years ago

Hello,

When I process a rice GEO file (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4471), it gives the following errors. Anyone know how to solve it?

library(affy); library(simpleaffy); library(affyPLM); library(ricecdf)

gse4471 <- ReadAffy(celfile.path=paste0("GSE4471", "_RAW"))

mas4471 <- call.exprs(gse4471, "mas5")

qc4471 <- qc(gse4471, mas4471)
Error in setQCEnvironment(cdfn) : 
  Could not find array definition file ' ricecdf.qcdef '. Simpleaffy does not know the QC parameters for this array type.
See the package vignette for details about how to specify QC parameters manually.

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /usr/lib64/libblas.so.3.4.2
LAPACK: /usr/lib64/liblapack.so.3.4.2

locale:
[1] C

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

other attached packages:
[1] ricecdf_2.18.0        affyPLM_1.56.0        preprocessCore_1.42.0
[4] simpleaffy_2.56.0     gcrma_2.52.0          genefilter_1.62.0    
[7] affy_1.58.0           Biobase_2.40.0        BiocGenerics_0.26.0  

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16         AnnotationDbi_1.42.0 XVector_0.20.0      
 [4] splines_3.5.0        zlibbioc_1.26.0      IRanges_2.14.1      
 [7] bit_1.1-12           lattice_0.20-35      xtable_1.8-2        
[10] blob_1.1.1           tools_3.5.0          grid_3.5.0          
[13] DBI_1.0.0            survival_2.42-3      bit64_0.9-7         
[16] digest_0.6.15        affyio_1.50.0        Matrix_1.2-14       
[19] S4Vectors_0.18.1     bitops_1.0-6         RCurl_1.95-4.10     
[22] memoise_1.1.0        RSQLite_2.1.1        compiler_3.5.0      
[25] BiocInstaller_1.30.0 Biostrings_2.48.0    stats4_3.5.0        
[28] XML_3.98-1.11        annotate_1.58.0     

Regards.

 

 

affymetrix qc • 680 views
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@james-w-macdonald-5106
Last seen 44 minutes ago
United States

The error you got said this:

Error in setQCEnvironment(cdfn) : 
  Could not find array definition file ' ricecdf.qcdef '. Simpleaffy does not know the QC parameters for this array type.
See the package vignette for details about how to specify QC parameters manually.

Which seems pretty clear. Did you read the simpleaffy vignette, particularly the part about how to set the QC parameters manually?

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Hello, I tried this, but still gives error.

> cdfName(gse4471)                                                                          
[1] "Rice"
> qc4471 <- qc(gse4471, mas4471, cdfn="Rice")                                               
Error in setQCEnvironment(cdfn) : 
  Could not find array definition file ' ricecdf.qcdef '. Simpleaffy does not know the QC parameters for this array type.
See the package vignette for details about how to specify QC parameters manually.

 

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But what does that have to do with what it says to do in the vignette? Here is a hint:

> dir(paste0(path.package("simpleaffy"), "/extdata"))
 [1] "atgenomecdf.qcdef"      "ath1121501cdf.qcdef"    "celeganscdf.qcdef"     
 [4] "drosgenome1cdf.qcdef"   "hcg110cdf.qcdef"        "hgfocuscdf.qcdef"      
 [7] "hgu133a2cdf.qcdef"      "hgu133acdf.qcdef"       "hgu133atagcdf.qcdef"   
[10] "hgu133bcdf.qcdef"       "hgu133plus2cdf.qcdef"   "hgu95acdf.qcdef"       
[13] "hgu95av2cdf.qcdef"      "hgu95bcdf.qcdef"        "hgu95ccdf.qcdef"       
[16] "hgu95dcdf.qcdef"        "hgu95ecdf.qcdef"        "mgu74acdf.qcdef"       
[19] "mgu74av2cdf.qcdef"      "mgu74bcdf.qcdef"        "mgu74bv2cdf.qcdef"     
[22] "mgu74ccdf.qcdef"        "mgu74cv2cdf.qcdef"      "moe430acdf.qcdef"      
[25] "mouse4302cdf.qcdef"     "mouse430a2cdf.qcdef"    "mouse430b2cdf.qcdef"   
[28] "mu11ksubacdf.qcdef"     "mu11ksubbcdf.qcdef"     "poplarcdf.qcdef"       
[31] "porcinecdf.qcdef"       "rae230acdf.qcdef"       "rae230bcdf.qcdef"      
[34] "rat2302cdf.qcdef"       "rgu34acdf.qcdef"        "rgu34bcdf.qcdef"       
[37] "rgu34ccdf.qcdef"        "rhesuscdf.qcdef"        "soybeancdf.qcdef"      
[40] "vitisviniferacdf.qcdef" "yeast2cdf.qcdef"        "ygs98cdf.qcdef"        
[43] "zebrafishcdf.qcdef"    

> read.delim(paste0(path.package("simpleaffy"), "/extdata/hgu133a2cdf.qcdef"))
                                                          array.hgu133a2cdf
1                                                              alpha1 0.05
2                                                             alpha2 0.065
3                                            spk bioB AFFX-r2-Ec-bioB-3_at
4                                            spk bioC AFFX-r2-Ec-bioC-3_at
5                                            spk bioD AFFX-r2-Ec-bioD-3_at
6                                             spk creX AFFX-r2-P1-cre-3_at
7      ratio actin3/actin5 AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_5_at
8      ratio actin3/actinM AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_M_at
9  ratio gapdh3/gapdh5 AFFX-HUMGAPDH/M33197_3_at AFFX-HUMGAPDH/M33197_5_at
10 ratio gapdh3/gapdhM AFFX-HUMGAPDH/M33197_3_at AFFX-HUMGAPDH/M33197_M_at

And it says how to make a qcdef file for a new array in the simpleaffy vignette, which is where I pointed you to begin with.

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Resolved. Thanks a lot.

Regards

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