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zhang.jianhai
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@zhangjianhai-12955
Last seen 5.0 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.
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.
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_atAnd 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.
Resolved. Thanks a lot.
Regards