Question: Problem Annotation Construction with pdInfoBuilder - Microarray Bioconductor
0
gravatar for thyagoleal
2.1 years ago by
thyagoleal0
thyagoleal0 wrote:

Hello, everyone.

I'm trying to create an annotation package to use with Oligo in analysis. I had provided the .xys file and a .ndf file as requested and I received the following error:

Building annotation package for Nimblegen Expression Array
NDF: GPL10191_090828_HG18.ndf
XYS: GSM597196_Nimblegen_Human_12-plex_434164_A12_MB6_.xys
=================================================================================
Parsing file: GPL10191_090828_HG18.ndf... OK
Parsing file: GSM597196_Nimblegen_Human_12-plex_434164_A12_MB6_.xys... OK
Merging NDF and XYS files... OK
Preparing contents for featureSet table... OK
Preparing contents for bgfeature table... OK
Preparing contents for pmfeature table... OK
Error in parseNgsPair(object@ndfFile, object@xysFile, verbose = !quiet) : 
  Control probe possibly identified as Experimental

Can anyone help me?

Thanks so much!

sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

locale: [1] LC_COLLATE=Portuguese_Brazil.1252 LC_CTYPE=Portuguese_Brazil.1252
[3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C
[5] LC_TIME=Portuguese_Brazil.1252

attached base packages: [1] grid stats4 parallel stats graphics grDevices utils
[8] datasets methods base

other attached packages: [1] pdInfoBuilder_1.38.0 affxparser_1.46.0 RSQLite_1.1-2
[4] HELP_1.32.0 Ringo_1.38.0 lattice_0.20-34
[7] Matrix_1.2-8 limma_3.30.11 RColorBrewer_1.1-2
[10] oligo_1.38.0 Biostrings_2.42.1 XVector_0.14.0
[13] IRanges_2.8.1 S4Vectors_0.12.1 Biobase_2.34.0
[16] oligoClasses_1.36.0 BiocGenerics_0.20.0

loaded via a namespace (and not attached): [1] Rcpp_0.12.9 plyr_1.8.4
[3] BiocInstaller_1.24.0 GenomeInfoDb_1.10.3
[5] bitops_1.0-6 iterators_1.0.8
[7] tools_3.3.2 zlibbioc_1.20.0
[9] digest_0.6.12 bit_1.1-12
[11] tibble_1.2 gtable_0.2.0
[13] annotate_1.52.1 memoise_1.0.0
[15] preprocessCore_1.36.0 ff_2.2-13
[17] foreach_1.4.3 DBI_0.5-1
[19] genefilter_1.56.0 AnnotationDbi_1.36.2
[21] survival_2.40-1 XML_3.98-1.5
[23] ggplot2_2.2.1 scales_0.4.1
[25] codetools_0.2-15 GenomicRanges_1.26.2
[27] splines_3.3.2 assertthat_0.1
[29] SummarizedExperiment_1.4.0 colorspace_1.3-2
[31] xtable_1.8-2 affy_1.52.0
[33] lazyeval_0.2.0 munsell_0.4.3
[35] RCurl_1.95-4.8 vsn_3.42.3
[37] affyio_1.44.0

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by thyagoleal0
0
gravatar for thyagoleal
2.1 years ago by
thyagoleal0
thyagoleal0 wrote:

Hey there, I fixed it by editing the .ndf file and replacing some probe mismatch values from > 10000 to 0. Now, I'll filter those out, before analysis.

ADD COMMENTlink written 2.1 years ago by thyagoleal0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1438 users visited in the last hour