Question: Problem Annotation Construction with pdInfoBuilder - Microarray Bioconductor
0
gravatar for sorghills
2.7 years ago by
sorghills0
sorghills0 wrote:

Hello, everyone.

I'm trying to create an annotation package to use with Oligo in microarray 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

I already checked if the files had unnecessary lines, restarted R, re-loaded only necessary packages, cleaned unused objects from environment, and double-checked code syntax.

Can anyone help me?

Thank you 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 2.7 years ago • written 2.7 years ago by sorghills0
Answer: Problem Annotation Construction with pdInfoBuilder - Microarray Bioconductor
0
gravatar for sorghills
2.7 years ago by
sorghills0
sorghills0 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 2.7 years ago by sorghills0
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 16.09
Traffic: 195 users visited in the last hour