Question

我刚刚将我的DESeq2软件包从版本1.4.5更新到版本1.6.3，我的脚本不再有效。具体来说，在使用函数DESeqDataSet生成DESeqDataSetFromMatrix对象时出现以下错误：

Error in validObject(.Object) :
invalid class “GRangesList” object: number of rows in DataTable 'mcols(x)' must match length of 'x'

要复制此错误，可以使用DESeq2晕影中显示的示例：

library("pasilla")
library("Biobase")
data("pasillaGenes")
countData <- counts(pasillaGenes)
colData <- pData(pasillaGenes)[,c("condition","type")]
dds <- DESeqDataSetFromMatrix(countData = countData,
                              colData = colData,
                              design = ~ condition)

或DESeq2参考手册中显示的示例：

 countData <- matrix(1:4,ncol=2)
 colData <- data.frame(condition=factor(c("a","b")))
 dds <- DESeqDataSetFromMatrix(countData, colData, formula(~ condition))

先谢谢你的帮助，

阿莱西娅

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  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] DESeq2_1.6.3            RcppArmadillo_0.4.400.0 Rcpp_0.11.2
[4] GenomicRanges_1.16.4    GenomeInfoDb_1.0.2      IRanges_1.22.10
[7] S4Vectors_0.4.0         BiocGenerics_0.12.1     BiocInstaller_1.16.1

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3      annotate_1.42.1      AnnotationDbi_1.26.0
 [4] BatchJobs_1.3        BBmisc_1.7           Biobase_2.24.0
 [7] BiocParallel_0.6.1   brew_1.0-6           checkmate_1.4
[10] cluster_1.15.3       codetools_0.2-9      colorspace_1.2-4
[13] DBI_0.3.0            digest_0.6.4         fail_1.2
[16] foreach_1.4.2        foreign_0.8-61       Formula_1.1-2
[19] genefilter_1.46.1    geneplotter_1.42.0   ggplot2_1.0.0
[22] grid_3.1.0           gtable_0.1.2         Hmisc_3.14-5
[25] iterators_1.0.7      lattice_0.20-29      latticeExtra_0.6-26
[28] locfit_1.5-9.1       MASS_7.3-34          munsell_0.4.2
[31] nnet_7.3-8           plyr_1.8.1           proto_0.3-10
[34] RColorBrewer_1.0-5   reshape2_1.4         rpart_4.1-8
[37] RSQLite_0.11.4       scales_0.2.4         sendmailR_1.1-2
[40] splines_3.1.0        stringr_0.6.2        survival_2.37-7
[43] tools_3.1.0          XML_3.98-1.1         xtable_1.7-4
[46] XVector_0.4.0


source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help

DESeq2 - 无效的类“GRangesList”对象

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