[BioC] DEXSeqDataSet

[Alejandro Reyes]

Dear Hatice,

Please ignore my previous e-mail, I misunderstood the problem!

You were right, the function was (incorrectly) throwing an error if the 
rownames of the count matrix were NULL.  I fixed this issue in the 
latest version in the svn.

Best regards,
Alejandro

> 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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>
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