Entering edit mode
@lykhenkoolexandr-13497
Last seen 3.2 years ago
I have downloaded from ArrayExpress raw data for microarray experiment E-GEOD-14722 (GSE14722):
aeData = getAE("E-GEOD-14722", type = 'raw')
and turned it into an ExpressionSet object. In fact, a list of two object, since the experiment uses two platforms.
affyData = ae2bioc(mageFiles = aeData)
Now I want to set custom platform annotation for this ExpressionSet object and use it to get expression matrix:
affyData1 = affyData[[1]] affyData1@annotation = "hgu133bhsentrezg.db" eset.br = rma(affyData1)
But I get the following error:
Loading required package: AnnotationDbi Loading required package: org.Hs.eg.db Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘pmindex’ for signature ‘"ChipDb"’ In addition: Warning message: In rsqlite_fetch(res@ptr, n = n) : Don't need to call dbFetch() for statements, only for queries
while everything works fine with native Affymetrix annotation.
How to properly set custom annotation for ExpressionSet object?
Here is sessioninfo()
R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.2 LTS Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/libopenblasp-r0.2.18.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods [9] base other attached packages: [1] hgu133bhsentrezg.db_22.0.0 org.Hs.eg.db_3.4.1 AnnotationDbi_1.38.1 [4] pd.hg.u133a_3.12.0 pd.hg.u133b_3.12.0 DBI_0.7 [7] oligo_1.40.1 RSQLite_2.0 Biostrings_2.44.1 [10] XVector_0.16.0 IRanges_2.10.2 S4Vectors_0.14.3 [13] ArrayExpress_1.36.0 cowplot_0.7.0 ggfortify_0.4.1 [16] ggplot2_2.2.1 stringr_1.2.0 sva_3.24.4 [19] BiocParallel_1.10.1 genefilter_1.58.1 mgcv_1.8-17 [22] nlme_3.1-131 affy_1.54.0 Biobase_2.36.2 [25] BiocGenerics_0.22.0 oligoClasses_1.38.0 loaded via a namespace (and not attached): [1] tidyr_0.6.3 bit64_0.9-7 splines_3.4.0 [4] foreach_1.4.3 assertthat_0.2.0 blob_1.1.0 [7] GenomeInfoDbData_0.99.0 lattice_0.20-35 glue_1.1.1 [10] limma_3.32.2 digest_0.6.12 GenomicRanges_1.28.3 [13] colorspace_1.3-2 preprocessCore_1.38.1 Matrix_1.2-10 [16] plyr_1.8.4 XML_3.98-1.9 pkgconfig_2.0.1 [19] affxparser_1.48.0 zlibbioc_1.22.0 xtable_1.8-2 [22] scales_0.4.1 affyio_1.46.0 ff_2.2-13 [25] tibble_1.3.3 annotate_1.54.0 SummarizedExperiment_1.6.3 [28] lazyeval_0.2.0 survival_2.41-3 magrittr_1.5 [31] memoise_1.1.0 BiocInstaller_1.26.0 tools_3.4.0 [34] matrixStats_0.52.2 munsell_0.4.3 DelayedArray_0.2.7 [37] bindrcpp_0.2 compiler_3.4.0 GenomeInfoDb_1.12.2 [40] rlang_0.1.1 grid_3.4.0 RCurl_1.95-4.8 [43] iterators_1.0.8 bitops_1.0-6 gtable_0.2.0 [46] codetools_0.2-15 R6_2.2.2 gridExtra_2.2.1 [49] dplyr_0.7.1 bit_1.1-12 bindr_0.1 [52] stringi_1.1.5 Rcpp_0.12.11
Thank you James W. MacDonald for suggested solution. I couldn't not find out however what was paremeter
target="mps1"for inThe interpreter says that this parameter is unused.
Well, it didn't say that in the code I posted, so your best recourse would be to carefully compare what I did versus what you did, and figure out where you went wrong.