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Question: rice affymetrix qc() function
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gravatar for zhang.jianhai
6 months ago by
zhang.jianhai0 wrote:

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.

 

 

ADD COMMENTlink modified 6 months ago by James W. MacDonald48k • written 6 months ago by zhang.jianhai0
0
gravatar for James W. MacDonald
6 months ago by
United States
James W. MacDonald48k wrote:

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?

ADD COMMENTlink written 6 months ago by James W. MacDonald48k

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.

 

ADD REPLYlink written 6 months ago by zhang.jianhai0

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.

ADD REPLYlink written 6 months ago by James W. MacDonald48k

Resolved. Thanks a lot.

Regards

ADD REPLYlink written 6 months ago by zhang.jianhai0
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