Hi,
I am new to microarray data analysis, trying to put the pieces of puzzle together. Trying to read raw Illumina Human HT-12 v4 data using beadarray. My raw data folder contains csv, txt, EIF, idat, locs, tif, xml file for each of the 12 samples. There is one sdf file, one metrics.txt file and 3 fiducial #N_Red_center.tif files.
Function readIllumina(useImages = FALSE, illuminaAnnotation = "Humanv4") gives the error below. Each txt file contains only two columns: Code Grn. Is the format of my raw data unsuitable for readIllumina? Or is there a way to instruct it so that it read the data properly? Thanks in advance!
Trying to read all Illumina files inD:\RData\HA1
Processing section 9992405085_A
Error in `[.data.frame`(lines, 1, 1:4) : undefined columns selected
> traceback()
6: stop("undefined columns selected")
5: `[.data.frame`(lines, 1, 1:4)
4: lines[1, 1:4]
3: numberOfColumns(file, sep = sep)
2: readBeadLevelTextFile(file.path(targets$directory[i], targets$textFile[i]),
dec = dec)
1: readIllumina(useImages = FALSE, illuminaAnnotation = "Humanv4")
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] beadarray_2.16.0 ggplot2_1.0.0 GEOquery_2.32.0
[4] lumi_2.18.0 Biobase_2.26.0 BiocGenerics_0.12.1
loaded via a namespace (and not attached):
[1] affy_1.44.0 affyio_1.34.0 annotate_1.44.0
[4] AnnotationDbi_1.28.1 base64_1.1 base64enc_0.1-2
[7] BatchJobs_1.5 BBmisc_1.8 BeadDataPackR_1.18.0
[10] beanplot_1.2 BiocInstaller_1.16.1 BiocParallel_1.0.0
[13] biomaRt_2.22.0 Biostrings_2.34.1 bitops_1.0-6
[16] brew_1.0-6 bumphunter_1.6.0 checkmate_1.5.1
[19] codetools_0.2-10 colorspace_1.2-4 DBI_0.3.1
[22] digest_0.6.8 doRNG_1.6 fail_1.2
[25] foreach_1.4.2 genefilter_1.48.1 GenomeInfoDb_1.2.4
[28] GenomicAlignments_1.2.1 GenomicFeatures_1.18.3 GenomicRanges_1.18.4
[31] grid_3.1.2 gtable_0.1.2 illuminaio_0.8.0
[34] IRanges_2.0.1 iterators_1.0.7 KernSmooth_2.23-13
[37] lattice_0.20-29 limma_3.22.4 locfit_1.5-9.1
[40] MASS_7.3-37 Matrix_1.1-5 matrixStats_0.13.1
[43] mclust_4.4 methylumi_2.12.0 mgcv_1.8-4
[46] minfi_1.12.0 multtest_2.22.0 munsell_0.4.2
[49] nleqslv_2.5 nlme_3.1-119 nor1mix_1.2-0
[52] pkgmaker_0.22 plyr_1.8.1 preprocessCore_1.28.0
[55] proto_0.3-10 quadprog_1.5-5 R.methodsS3_1.6.1
[58] RColorBrewer_1.1-2 Rcpp_0.11.4 RCurl_1.95-4.5
[61] registry_0.2 reshape_0.8.5 reshape2_1.4.1
[64] rngtools_1.2.4 Rsamtools_1.18.2 RSQLite_1.0.0
[67] rtracklayer_1.26.2 S4Vectors_0.4.0 scales_0.2.4
[70] sendmailR_1.2-1 siggenes_1.40.0 splines_3.1.2
[73] stats4_3.1.2 stringr_0.6.2 survival_2.37-7
[76] tools_3.1.2 XML_3.98-1.1 xtable_1.7-4
[79] XVector_0.6.0 zlibbioc_1.12.0
Jaro
Jaroslav Slamecka, PhD.
Mitchell Cancer Institute
University of South Alabama
1660 Springhill Ave.
Mobile, AL 36604