[BioC] DEXSeqDataSet

[Alejandro Reyes]

Dear Hatice,

The error is probably because the dimension of your input objects does 
not match... You have to make sure that the length of the groupIDs and 
featureIDs coresponds to the number of rows of your count matrix.  You 
also have to make sure that the number of rows of your sampleData 
data.frame corresponds to the number of columns of your count data.

Do you know if this is the case?

Best regards,
Alejandro

> Hello,
>
> First of all, thank you for developing and maintaining this great package.
>
> I am trying to create DEXSeqDataSet by following the example from manual.
>
> countData <- matrix( rpois(10000, 100), nrow=1000 )
> sampleData <- data.frame(
> condition=rep( c("untreated", "treated"), each=5 ) )
> design <- formula( ~ sample + exon + condition:exon )
> groupID <- rep(
> sprintf("gene
> each= 100 )
> featureID <- rep(
> sprintf("exon
> times= 100 )
> DEXSeqDataSet( countData, sampleData, design,
> featureID, groupID )
>
> There is something missing regarding to featureID and groupID.
>
> For my code
> library(DEXSeq)
> library(parallel)
> #newData <-
> data[,c(which(Basal.index),which(Her2.index),which(LumA.index),which(LumB.index))]
> condition =
> c(rep('LumA',length(which(LumA.index))),rep('LumB',length(which(LumB.index))))
> newData <- data[,c(which(LumA.index),which(LumB.index))]
> newData <- sapply(newData, as.numeric)
> # > dim(newData)
> # [1] 224158    357
> #cds = newExonCountSet(newData, condition, gene.ids, exon.ids )
> design <- formula( ~ sample + exon + condition:exon )
> sampleData = data.frame(condition)
> rownames(sampleData) <- colnames(newData)
> featureID = exon.ids
> groupID = gene.ids
> cds = DEXSeqDataSet(newData, sampleData,
>                      design,
>                      featureID, groupID)
>
> But always receiving following error:
> Error in .Method(..., deparse.level = deparse.level) :
>    number of rows of matrices must match (see arg 2)
>
> How can I fix this error?
>
> Thank you for your assistance in advance.
>
> Best,
> Hatice
>
>> sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] DEXSeq_1.10.0           BiocParallel_0.6.0      DESeq2_1.4.1
>   [4] RcppArmadillo_0.4.300.0 Rcpp_0.11.1             GenomicRanges_1.16.1
>   [7] GenomeInfoDb_1.0.2      IRanges_1.22.6          Biobase_2.24.0
> [10] BiocGenerics_0.10.0
>
> loaded via a namespace (and not attached):
>   [1] annotate_1.42.0      AnnotationDbi_1.26.0 BatchJobs_1.2
>   [4] BBmisc_1.5           biomaRt_2.20.0       Biostrings_2.32.0
>   [7] bitops_1.0-6         brew_1.0-6           codetools_0.2-8
> [10] DBI_0.2-7            digest_0.6.4         fail_1.2
> [13] foreach_1.4.2        genefilter_1.46.0    geneplotter_1.42.0
> [16] grid_3.1.0           hwriter_1.3          iterators_1.0.7
> [19] lattice_0.20-29      locfit_1.5-9.1       plyr_1.8.1
> [22] RColorBrewer_1.0-5   RCurl_1.95-4.1       Rsamtools_1.16.0
> [25] RSQLite_0.11.4       sendmailR_1.1-2      splines_3.1.0
> [28] statmod_1.4.19       stats4_3.1.0         stringr_0.6.2
> [31] survival_2.37-7      tools_3.1.0          XML_3.98-1.1
> [34] xtable_1.7-3         XVector_0.4.0        zlibbioc_1.10.0
>
> 	[[alternative HTML version deleted]]
>
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