本人刚刚开始接触生物信息学领域，正在做胃肠道肿瘤中相关基因表达差异分析，下载了TCGA数据库中RNA-Seq的count数据，利用TCGA建议下载工具对全部样本进行了处理合并生成了Merge文件，用DECenter中的edgeR实现了差异表达的分析，现在想用DESeq2模块再分析一遍，但是在运行中出现了报错情况，软件具体运行过程如下，请问应该怎样处理此种情况：
运行R命令：F:\Postgraduate\ShengXinToolBox\source\softs\R-Portable\App\R-Portable\bin\Rscript.exe F:\dec_tmp_bak\limma.R F:\dec_tmp_bak DESeq2 matrix.xls sample.xls 1 0.05
载入需要的程辑包：DESeq2
Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help
A newer version of Bioconductor is available for this version of R,
?BiocUpgrade for help
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Installing package(s) 'DESeq2'
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
无法打开URL'https://cran.rstudio.com/src/contrib/PACKAGES'
Warning: dependencies 'ggplot2', 'Hmisc', 'Rcpp', 'RcppArmadillo', 'RColorBrewer' are not available
also installing the dependencies 'annotate', 'S4Vectors', 'IRanges', 'GenomicRanges', 'SummarizedExperiment', 'BiocGenerics', 'Biobase', 'BiocParallel', 'genefilter', 'geneplotter'
Warning: unable to access index for repository https://cran.rstudio.com/bin/windows/contrib/3.4:
无法打开URL'https://cran.rstudio.com/bin/windows/contrib/3.4/PACKAGES'
试开URL’https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/annotate_1.54.0.zip'
Content type 'application/zip' length 3916193 bytes (3.7 MB)
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downloaded 3.7 MB
试开URL’https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/S4Vectors_0.14.7.zip'
Content type 'application/zip' length 2648696 bytes (2.5 MB)
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downloaded 2.5 MB
试开URL’https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/IRanges_2.10.5.zip'
Content type 'application/zip' length 3032811 bytes (2.9 MB)
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downloaded 2.9 MB
试开URL’https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/GenomicRanges_1.28.6.zip'
Content type 'application/zip' length 2998648 bytes (2.9 MB)
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downloaded 2.9 MB
试开URL’https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/SummarizedExperiment_1.6.5.zip'
Content type 'application/zip' length 2933786 bytes (2.8 MB)
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downloaded 2.8 MB
试开URL’https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/BiocGenerics_0.22.1.zip'
Content type 'application/zip' length 1155336 bytes (1.1 MB)
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downloaded 1.1 MB
试开URL’https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/Biobase_2.36.2.zip'
Content type 'application/zip' length 4241291 bytes (4.0 MB)
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downloaded 4.0 MB
试开URL’https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/BiocParallel_1.10.1.zip'
Content type 'application/zip' length 1360536 bytes (1.3 MB)
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downloaded 1.3 MB
试开URL’https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/genefilter_1.58.1.zip'
Content type 'application/zip' length 2683945 bytes (2.6 MB)
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downloaded 2.6 MB
试开URL’https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/geneplotter_1.54.0.zip'
Content type 'application/zip' length 3002598 bytes (2.9 MB)
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downloaded 2.9 MB
试开URL’https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/DESeq2_1.16.1.zip'
Content type 'application/zip' length 4459785 bytes (4.3 MB)
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downloaded 4.3 MB
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
无法打开URL'https://cran.rstudio.com/src/contrib/PACKAGES'
Old packages: 'limma'
载入需要的程辑包：DESeq2
载入需要的程辑包：S4Vectors
载入需要的程辑包：methods
载入需要的程辑包：stats4
载入需要的程辑包：BiocGenerics
载入需要的程辑包：parallel
载入程辑包：'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which, which.max, which.min
载入程辑包：'S4Vectors'
The following object is masked from 'package:base':
expand.grid
载入需要的程辑包：IRanges
载入需要的程辑包：GenomicRanges
载入需要的程辑包：GenomeInfoDb
Error: package or namespace load failed for 'GenomeInfoDb' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
不存在叫'GenomeInfoDbData'这个名字的程辑包
Failed with error: '无法载入程辑包'GenomeInfoDb''
此外: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
不存在叫'DESeq2'这个名字的程辑包
2: 程辑包'GenomicRanges'是用R版本3.4.2 来建造的
3: 程辑包'GenomeInfoDb'是用R版本3.4.2 来建造的
package 'annotate' successfully unpacked and MD5 sums checked
package 'S4Vectors' successfully unpacked and MD5 sums checked
package 'IRanges' successfully unpacked and MD5 sums checked
package 'GenomicRanges' successfully unpacked and MD5 sums checked
package 'SummarizedExperiment' successfully unpacked and MD5 sums checked
package 'BiocGenerics' successfully unpacked and MD5 sums checked
package 'Biobase' successfully unpacked and MD5 sums checked
package 'BiocParallel' successfully unpacked and MD5 sums checked
package 'genefilter' successfully unpacked and MD5 sums checked
package 'geneplotter' successfully unpacked and MD5 sums checked
package 'DESeq2' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Administrator\AppData\Local\Temp\RtmpmsAVPl\downloaded_packages
ERROR : 没有"DESeqDataSetFromMatrix"这个函数
