Hello,
I have an inquiry on how to apply the "paCalls" function of the oligo package. I received a wicked error message after running the "paCalls(CELdat, "PSDABG")" line which states:
Computing DABG calls... Error in 0:max(counts) : result would be too long a vector
In addition: Warning message:
In max(counts) : no non-missing arguments to max; returning -Inf
I am unsure how to interpret this message; obviously the resulting vector is really long but how long is too long? Can anyone provide some insight as to what's going on here, and how I might fix it? Thanks in advance. Best,
- Matt
library(oligo) setwd("C:\\...\\microarray") CELlist <- list.celfiles("C:\\...\\microarray\\CEL", full.names=TRUE, pattern=NULL, all.file=FALSE) pdat<-read.AnnotatedDataFrame("C:\\...\\x.txt",header=TRUE,row.name="Filename",sep="\t") CELdat <- read.celfiles(filenames = CELlist,experimentData=TRUE,phenoData=pdat,verbose=TRUE) > CELdat GeneFeatureSet (storageMode: lockedEnvironment) assayData: 1416100 features, 16 samples element names: exprs protocolData rowNames: WT1 WT2 ... RS4 (16 total) varLabels: exprs dates varMetadata: labelDescription channel phenoData rowNames: WT1 WT2 ... RS4 (16 total) varLabels: Sample Treatment ... BATCH_GROUP (6 total) varMetadata: labelDescription channel featureData: none experimentData: use 'experimentData(object)' Annotation: pd.zebgene.1.1.st > paCalls(CELdat, "PSDABG") Computing DABG calls... Error in 0:max(counts) : result would be too long a vector In addition: Warning message: In max(counts) : no non-missing arguments to max; returning -Inf
> sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 16299) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods [9] base other attached packages: [1] pd.zebgene.1.1.st_3.12.0 DBI_0.7 RSQLite_2.0 [4] oligo_1.40.2 Biostrings_2.44.2 XVector_0.16.0 [7] IRanges_2.10.2 S4Vectors_0.14.3 Biobase_2.36.2 [10] oligoClasses_1.38.0 BiocGenerics_0.22.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.12 compiler_3.4.1 BiocInstaller_1.26.1 [4] GenomeInfoDb_1.12.2 bitops_1.0-6 iterators_1.0.8 [7] tools_3.4.1 zlibbioc_1.22.0 digest_0.6.12 [10] bit_1.1-12 memoise_1.1.0 tibble_1.3.3 [13] preprocessCore_1.38.1 lattice_0.20-35 ff_2.2-13 [16] pkgconfig_2.0.1 rlang_0.1.1 Matrix_1.2-10 [19] foreach_1.4.3 DelayedArray_0.2.7 GenomeInfoDbData_0.99.0 [22] affxparser_1.48.0 bit64_0.9-7 grid_3.4.1 [25] blob_1.1.0 splines_3.4.1 codetools_0.2-15 [28] matrixStats_0.52.2 GenomicRanges_1.28.4 SummarizedExperiment_1.6.3 [31] RCurl_1.95-4.8 affyio_1.46.0