Dear Community,
based on the code presented on a previous post, regarding the import and analysis of Affymetrix Human ST 2.0 microarrays (Preprocessing of Human Gene 2.0 ST microarrays with oligo R package and annotation options), i tried to create some exploratory diagnostic plots regarding the success of normalization, for a needed report:
library(oligo)
library(affycoretools)
library(hugene20sttranscriptcluster.db)
library(limma)
librarypd.hugene.2.0.st)
setwd(mydir)
pdat <- read.table("pdat.project.txt",header=TRUE,stringsAsFactors = FALSE) # phenotype info
celfiles = list.celfiles()
affyRaw <- read.celfiles(celfiles)
identical(colnames(affyRaw),rownames(pdat)) # need to be identical for incorporate phenotype info
[1] TRUE
pd <- AnnotatedDataFrame(data= pdat)
phenoData(affyRaw) <- pd
celfiles.rma <- rma(affy.cels, target="probeset")
But then when i tried:
par(mfrow=c(1,2))
boxplot(affyRaw, col = cols, target="core",las = 2, main = "Pre-Normalization");
Error in `$<-.data.frame`(`*tmp*`, "channel", value = integer(0)) :
replacement has 0 rows, data has 2
boxplot(celfiles.rma, col = cols, las = 2, main = "Post-Normalization")
Any ideas or suggestions about this weird error ?
affyRaw
GeneFeatureSet (storageMode: lockedEnvironment)
assayData: 2598544 features, 6 samples
element names: exprs
protocolData
rowNames: Eogh1_DN41.CEL Eogh1_DN42.CEL ... Eogh1_MN243.CEL (6 total)
varLabels: exprs dates
varMetadata: labelDescription channel
phenoData
rowNames: Eogh1_DN41.CEL Eogh1_DN42.CEL ... Eogh1_MN243.CEL (6 total)
varLabels: Condition Batch
varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.hugene.2.0.st
sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
locale:
[1] LC_COLLATE=Greek_Greece.1253 LC_CTYPE=Greek_Greece.1253
[3] LC_MONETARY=Greek_Greece.1253 LC_NUMERIC=C
[5] LC_TIME=Greek_Greece.1253
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] RColorBrewer_1.1-2 pd.hugene.2.0.st_3.14.1
[3] DBI_0.5-1 RSQLite_1.1-2
[5] limma_3.28.21 hugene20sttranscriptcluster.db_8.4.0
[7] org.Hs.eg.db_3.3.0 AnnotationDbi_1.34.4
[9] affycoretools_1.44.3 oligo_1.36.1
[11] Biostrings_2.40.2 XVector_0.12.1
[13] IRanges_2.6.1 S4Vectors_0.10.3
[15] Biobase_2.32.0 oligoClasses_1.34.0
[17] BiocGenerics_0.18.0
loaded via a namespace (and not attached):
[1] colorspace_1.3-2 hwriter_1.3.2
[3] biovizBase_1.20.0 htmlTable_1.9
[5] GenomicRanges_1.24.3 base64enc_0.1-3
[7] dichromat_2.0-0 affyio_1.42.0
[9] interactiveDisplayBase_1.10.3 codetools_0.2-15
[11] splines_3.3.1 R.methodsS3_1.7.1
[13] ggbio_1.20.2 geneplotter_1.50.0
[15] knitr_1.15.1 Formula_1.2-1
[17] Rsamtools_1.24.0 annotate_1.50.1
[19] cluster_2.0.5 GO.db_3.3.0
[21] R.oo_1.21.0 graph_1.50.0
[23] shiny_1.0.0 httr_1.2.1
[25] GOstats_2.38.1 backports_1.0.5
[27] assertthat_0.1 Matrix_1.2-8
[29] lazyeval_0.2.0 acepack_1.4.1
[31] htmltools_0.3.5 tools_3.3.1
[33] gtable_0.2.0 affy_1.50.0
[35] Category_2.38.0 reshape2_1.4.2
[37] affxparser_1.44.0 Rcpp_0.12.9
[39] gdata_2.17.0 preprocessCore_1.34.0
[41] rtracklayer_1.32.2 iterators_1.0.8
[43] stringr_1.1.0 mime_0.5
[45] ensembldb_1.4.7 gtools_3.5.0
[47] XML_3.98-1.5 AnnotationHub_2.4.2
[49] edgeR_3.14.0 zlibbioc_1.18.0
[51] scales_0.4.1 BSgenome_1.40.1
[53] VariantAnnotation_1.18.7 BiocInstaller_1.22.3
[55] SummarizedExperiment_1.2.3 RBGL_1.48.1
[57] memoise_1.0.0 gridExtra_2.2.1
[59] ggplot2_2.2.1 biomaRt_2.28.0
[61] rpart_4.1-10 reshape_0.8.6
[63] latticeExtra_0.6-28 stringi_1.1.2
[65] gcrma_2.44.0 genefilter_1.54.2
[67] foreach_1.4.3 checkmate_1.8.2
[69] caTools_1.17.1 GenomicFeatures_1.24.5
[71] BiocParallel_1.6.6 GenomeInfoDb_1.8.7
[73] ReportingTools_2.12.2 bitops_1.0-6
[75] lattice_0.20-34 GenomicAlignments_1.8.4
[77] htmlwidgets_0.8 bit_1.1-12
[79] GSEABase_1.34.1 AnnotationForge_1.14.2
[81] GGally_1.3.0 plyr_1.8.4
[83] magrittr_1.5 DESeq2_1.12.4
[85] R6_2.2.0 gplots_3.0.1
[87] Hmisc_4.0-2 foreign_0.8-67
[89] survival_2.40-1 RCurl_1.95-4.8
[91] nnet_7.3-12 tibble_1.2
[93] KernSmooth_2.23-15 OrganismDbi_1.14.1
[95] PFAM.db_3.3.0 locfit_1.5-9.1
[97] grid_3.3.1 data.table_1.10.4
[99] digest_0.6.12 xtable_1.8-2
[101] ff_2.2-13 httpuv_1.3.3
[103] R.utils_2.5.0 munsell_0.4.3

