使用xps和oligo分析Affymetrix Exon/Gene ST Arrays 26

首先安装xps和oligo。

安装oligo比较简单。直接

 source("http://www.bioconductor.org/biocLite.R")
 biocLite("oligo")

就可以了。

而安装xps可能麻烦一点,首先要安装ROOT,其主页为http://root.cern.ch/drupal/

而后是安装xps,为了确保安装效果,请使用:

 source("http://www.bioconductor.org/biocLite.R")
 biocLite("xps",type="source")

安装成功之后,就可以使用library(xps)调用了。

好了,我们先使用oligo来分析。

> library(oligo)
Loading required package: oligoClasses
Loading required package: Biobase
 
Welcome to Bioconductor
 
  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.
 
Attaching package: 'Biobase'
.....
Attaching package: 'oligo'
> geneCELs<-list.celfiles(full.names=T)
> geneCELs
[1] "./PAO-1_(RaGene-1_0-st-v1).CEL" "./PAO-2_(RaGene-1_0-st-v1).CEL" "./PAO-3_(RaGene-1_0-st-v1).CEL"
[4] "./PAR-1_(RaGene-1_0-st-v1).CEL" "./PAR-2_(RaGene-1_0-st-v1).CEL" "./PAR-3_(RaGene-1_0-st-v1).CEL"
>  affyGeneFS <- read.celfiles(geneCELs)
Loading required package: pd.ragene.1.0.st.v1
Loading required package: RSQLite
Loading required package: DBI
Platform design info loaded.
Reading in : ./PAO-1_(RaGene-1_0-st-v1).CEL
Reading in : ./PAO-2_(RaGene-1_0-st-v1).CEL
Reading in : ./PAO-3_(RaGene-1_0-st-v1).CEL
Reading in : ./PAR-1_(RaGene-1_0-st-v1).CEL
Reading in : ./PAR-2_(RaGene-1_0-st-v1).CEL
Reading in : ./PAR-3_(RaGene-1_0-st-v1).CEL
> affyGeneFS
GeneFeatureSet (storageMode: lockedEnvironment)
assayData: 1102500 features, 6 samples
  element names: exprs
protocolData
  rowNames: PAO-1_(RaGene-1_0-st-v1).CEL PAO-2_(RaGene-1_0-st-v1).CEL ...
    PAR-3_(RaGene-1_0-st-v1).CEL (6 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: PAO-1_(RaGene-1_0-st-v1).CEL PAO-2_(RaGene-1_0-st-v1).CEL ...
    PAR-3_(RaGene-1_0-st-v1).CEL (6 total)
  varLabels: index
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.ragene.1.0.st.v1
> # RMA - probeset level
> genePS <- rma(affyGeneFS, target = "probeset")
Background correcting
Normalizing
Calculating Expression
> # RMA - transcript level
> geneCore <- rma(affyGeneFS, target = "core")
Background correcting
Normalizing
Calculating Expression
> # For Exon arrays, there are three possible
> # options for transcript level summarization: core, full and extended. For Gene arrays, only
> # summaries for core probesets is available.

> # Retrieving NetAffx Biological Annotation
> genePS
ExpressionSet (storageMode: lockedEnvironment)
assayData: 213067 features, 6 samples
  element names: exprs
protocolData
  rowNames: PAO-1_(RaGene-1_0-st-v1).CEL PAO-2_(RaGene-1_0-st-v1).CEL ...
    PAR-3_(RaGene-1_0-st-v1).CEL (6 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: PAO-1_(RaGene-1_0-st-v1).CEL PAO-2_(RaGene-1_0-st-v1).CEL ...
    PAR-3_(RaGene-1_0-st-v1).CEL (6 total)
  varLabels: index
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.ragene.1.0.st.v1
>  featureData(genePS) <- getNetAffx(genePS, "probeset")
> genePS
ExpressionSet (storageMode: lockedEnvironment)
assayData: 213067 features, 6 samples
  element names: exprs
protocolData
  rowNames: PAO-1_(RaGene-1_0-st-v1).CEL PAO-2_(RaGene-1_0-st-v1).CEL ...
    PAR-3_(RaGene-1_0-st-v1).CEL (6 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: PAO-1_(RaGene-1_0-st-v1).CEL PAO-2_(RaGene-1_0-st-v1).CEL ...
    PAR-3_(RaGene-1_0-st-v1).CEL (6 total)
  varLabels: index
  varMetadata: labelDescription channel
featureData
  featureNames: 10700001 10700002 ... 10940690 (213067 total)
  fvarLabels: probesetid seqname ... probesettype (39 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: pd.ragene.1.0.st.v1
>  featureData(geneCore) <- getNetAffx(geneCore, "transcript")
> geneCore
ExpressionSet (storageMode: lockedEnvironment)
assayData: 29214 features, 6 samples
  element names: exprs
protocolData
  rowNames: PAO-1_(RaGene-1_0-st-v1).CEL PAO-2_(RaGene-1_0-st-v1).CEL ...
    PAR-3_(RaGene-1_0-st-v1).CEL (6 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: PAO-1_(RaGene-1_0-st-v1).CEL PAO-2_(RaGene-1_0-st-v1).CEL ...
    PAR-3_(RaGene-1_0-st-v1).CEL (6 total)
  varLabels: index
  varMetadata: labelDescription channel
featureData
  featureNames: 10700001 10700002 ... 10940690 (29214 total)
  fvarLabels: transcriptclusterid probesetid ... category (18 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: pd.ragene.1.0.st.v1

至此,我们手头就有了基因水平的表达结果,其后就可以使用limma来获得差异表达的基因了。

我们使用xps来分析。

> library(xps)
 
Welcome to xps version 1.12.1
    an R wrapper for XPS - eXpression Profiling System
    (c) Copyright 2001-2011 by Christian Stratowa
 
Attaching package: 'xps'
 
The following object(s) are masked from 'package:stats':
 
    residuals, weights
 
> dir<-"/Users/jianhongou/Documents/Fumihiko/2011-08-23"
> setwd(dir)
> celfiles<-dir(pattern=".cel",ignore.case=T)
> celfiles
[1] "PAO-1_(RaGene-1_0-st-v1).CEL" "PAO-2_(RaGene-1_0-st-v1).CEL" "PAO-3_(RaGene-1_0-st-v1).CEL" "PAR-1_(RaGene-1_0-st-v1).CEL"
[5] "PAR-2_(RaGene-1_0-st-v1).CEL" "PAR-3_(RaGene-1_0-st-v1).CEL"
> libdir <- "/opt/local/apache2/htdocs/eam/RaGene-1_0-st-v1"
> scheme.ragene10stv1r4 <- import.exon.scheme("Scheme_RaGene10stv1r4",
+                                layoutfile=paste(libdir,"RaGene-1_0-st-v1.r4.clf",sep="/"),
+                                schemefile=paste(libdir,"RaGene-1_0-st-v1.r4.pgf",sep="/"),
+                                probeset=paste(libdir,"RaGene-1_0-st-v1.na31.rn4.probeset.csv",sep="/"),
+                                transcript=paste(libdir,"RaGene-1_0-st-v1.na31.rn4.transcript.csv",sep="/"))
Creating new file </Users/jianhongou/Scheme_RaGene10stv1r4.root>...
Importing </opt/local/apache2/htdocs/eam/RaGene-1_0-st-v1/RaGene-1_0-st-v1.r4.clf> as <RaGene-1_0-st-v1.cxy>...
   <1102500> records imported...Finished
New dataset <RaGene-1_0-st-v1> is added to Content...
Importing </opt/local/apache2/htdocs/eam/RaGene-1_0-st-v1/RaGene-1_0-st-v1.na31.rn4.probeset.csv> as <RaGene-1_0-st-v1.anp>...
Note: The following header columns are missing or in wrong order:
   <mouse_fl>
   <mouse_mrna>
   <rat_fl>
   <rat_mrna>
   Number of probesets is <213067>.
   Number of annotated transcripts is <29214>.
   <29214> records read...Finished14>.
   <28041> records imported...Finished
 
> celnames<-gsub("\\(RaGene-1_0-st-v1\\).CEL","",celfiles)
> celnames
[1] "PAO-1_" "PAO-2_" "PAO-3_" "PAR-1_" "PAR-2_" "PAR-3_"
> data <- import.data(scheme.ragene10stv1r4,filename="tmpdt_Data",filedir=dir,celdir=dir,celfiles=celfiles,celnames=celnames)
Opening file </Users/jianhongou/Documents/Fumihiko/2011-08-23/Scheme_RaGene10stv1r4.root> in <READ> mode...
Creating new temporary file </Users/jianhongou/Documents/Fumihiko/2011-08-23/tmpdt_Data_cel_20110824_173559.root>...
Importing </Users/jianhongou/Documents/Fumihiko/2011-08-23/PAO-1_(RaGene-1_0-st-v1).CEL> as <PAO_1_.cel>...
   hybridization statistics:
      1 cells with minimal intensity 23
      3 cells with maximal intensity 65534
New dataset <DataSet> is added to Content...
Importing </Users/jianhongou/Documents/Fumihiko/2011-08-23/PAO-2_(RaGene-1_0-st-v1).CEL> as <PAO_2_.cel>...
   hybridization statistics:
      1 cells with minimal intensity 24
      1 cells with maximal intensity 63204
Importing </Users/jianhongou/Documents/Fumihiko/2011-08-23/PAO-3_(RaGene-1_0-st-v1).CEL> as <PAO_3_.cel>...
   hybridization statistics:
      1 cells with minimal intensity 22
      1 cells with maximal intensity 36841
Importing </Users/jianhongou/Documents/Fumihiko/2011-08-23/PAR-1_(RaGene-1_0-st-v1).CEL> as <PAR_1_.cel>...
   hybridization statistics:
      2 cells with minimal intensity 23
      1 cells with maximal intensity 65533
Importing </Users/jianhongou/Documents/Fumihiko/2011-08-23/PAR-2_(RaGene-1_0-st-v1).CEL> as <PAR_2_.cel>...
   hybridization statistics:
      2 cells with minimal intensity 23
      2 cells with maximal intensity 65534
Importing </Users/jianhongou/Documents/Fumihiko/2011-08-23/PAR-3_(RaGene-1_0-st-v1).CEL> as <PAR_3_.cel>...
Warning message:
In import.data(scheme.ragene10stv1r4, filename = "tmpdt_Data", filedir = dir,  :
  characters [](){}.:# etc in 'celnames' will be replaced  with '_'
   hybridization statistics:
      5 cells with minimal intensity 26
      17 cells with maximal intensity 65534
> data <- attachInten(data)
> temp <- intensity(data)
> head(temp)
  X Y PAO_1__RaGene_1_0_st_v1_.cel_MEAN PAO_2__RaGene_1_0_st_v1_.cel_MEAN PAO_3__RaGene_1_0_st_v1_.cel_MEAN
1 0 0                              8485                              6825                              8915
2 1 0                               290                               197                               233
3 2 0                              9184                              7000                              8774
4 3 0                               279                               191                               184
5 4 0                                52                                58                                66
6 5 0                               174                               127                               137
  PAR_1__RaGene_1_0_st_v1_.cel_MEAN PAR_2__RaGene_1_0_st_v1_.cel_MEAN PAR_3__RaGene_1_0_st_v1_.cel_MEAN
1                              7683                              9576                              7932
2                               201                               259                               212
3                              7111                              9466                              7366
4                               183                               265                               152
5                                56                                86                                57
6                               173                               162                               220
> data<-attachMask(data)
> setwd(dir)
> png("hist.png",width=1024,height=1024)
> hist(data)
> dev.off()
quartz
     2 
 
> png("boxplot.png",width=1024,height=1024)
> boxplot(data)
> dev.off()
quartz
     2 
 
> png("pmplot.png",width=1024,height=1024)
> pmplot(data)
> dev.off()
quartz
     2 
 
> data<-removeInten(data)
> data<-removeMask(data)
> data.rma<-rma(data,"tmpdt_rma")

其余略。。。。

https://github.com/benilton/oligo/wiki/Getting-the-grips-with-the-oligo-Package

26 thoughts on “使用xps和oligo分析Affymetrix Exon/Gene ST Arrays

  1. Pingback: bioconductor系列教程之三–Affymetrix 外显子(exon)分析综合 | 糗世界

  2. Pingback: 使用xps分析affymetrix genechip ← 糗世界

  3. Reply R初学者 1月 21,2014 2:02 上午

    博主,您好,看了您的文章,想请教您,“而安装xps可能麻烦一点,首先要安装ROOT,其主页为http://root.cern.ch/drupal/”我下载了”root_v5.34.14.source.tar”,这个解压了就相当于安装了,是吗?还有这个要安装在哪里?是和R一个文件夹里吗?还有“糗世界”在哪里注册啊?

    • Reply admin 1月 21,2014 9:30 上午

      对,直接安装就好了。不需要在一个文件夹中,但是需要让系统能找到你安装的目录,具体在windows下我无法测试。糗世界无法注册。

  4. Reply zhenhua 8月 13,2014 8:35 上午

    至此,我们手头就有了基因水平的表达结果,其后就可以使用limma来获得差异表达的基因了。

    博主,有没有博文讲下一步limma的分析啊

  5. Reply taotao 8月 24,2014 10:20 下午

    博主您好,为什么执行代码genePS <- rma(affyGeneFS, target = "probeset")时候出现Error in .local(object, …) : unused argument (target = "probeset")

  6. Reply chunlan 11月 10,2014 11:57 上午

    欧博您好,
    我的出现错误了> affyGeneFS <- read.celfiles(geneCELs)
    All the CEL files must be of the same type.
    Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) ist nicht TRUE
    怎么办啊

    • Reply admin 11月 12,2014 2:00 下午

      检查你的CEL文件是不是都是相同的affymetrix公司的平台的数据。你可以直接使用文本文档打开CEL文件,查看最初几行,看看它们的型号是否一致。如果是来自于不同型号的芯片,分开分析。

  7. Reply chunlan 11月 10,2014 12:13 下午

    欧博,上个问题解决了,但是出现了新的错误>
    > affyGeneFS
    GeneFeatureSet (storageMode: lockedEnvironment)
    assayData: 1102500 features, 39 samples
    element names: exprs
    protocolData
    rowNames: GSM1085665_HE32H001.CEL GSM1085666_HE32H003.CEL …
    GSM1085703_HE32H040.CEL (39 total)
    varLabels: exprs dates
    varMetadata: labelDescription channel
    phenoData
    rowNames: GSM1085665_HE32H001.CEL GSM1085666_HE32H003.CEL …
    GSM1085703_HE32H040.CEL (39 total)
    varLabels: index
    varMetadata: labelDescription channel
    featureData: none
    experimentData: use ‘experimentData(object)’
    Annotation: pd.hugene.1.0.st.v1
    > # RMA – probeset level
    > genePS eset<-rma(affyGeneFS)

  8. Reply chunlan 11月 10,2014 12:15 下午

    新的错误》
    > # RMA – probeset level
    > genePS <- rma(affyGeneFS, target = "probeset")
    Error in (function (classes, fdef, mtable) :
    unable to find an inherited method for function ‘probeNames’ for signature ‘"GeneFeatureSet"’

  9. Reply amiee2406 1月 11,2015 10:59 上午

    欧博士,我用的是Mac系统(10.10.1),已经启用root用户,已下载root_v5.34.17.source.tar.gz,接下来应该如何安装root?

  10. Reply amiee2406 1月 19,2015 10:42 上午

    欧博士,
    geneCELs<-list.celfiles(full.names=T)
    data.raw <- read.celfiles(geneCELs)
    data.rma sessionInfo()
    R version 3.1.1 (2014-07-10)
    Platform: x86_64-apple-darwin13.1.0 (64-bit)

    locale:
    [1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8

    attached base packages:
    [1] parallel stats graphics grDevices utils methods base

    other attached packages:
    [1] hugene10sttranscriptcluster.db_8.1.0 hugene10stprobeset.db_8.1.0
    [3] hugene10stv1probe_2.14.0 org.Hs.eg.db_2.14.0
    [5] AnnotationDbi_1.26.1 GenomeInfoDb_1.0.2
    [7] affy_1.42.3 BiocInstaller_1.14.3
    [9] hugene10stv1cdf_2.14.0 pd.hugene.1.0.st.v1_3.8.0
    [11] RSQLite_1.0.0 DBI_0.3.1
    [13] RColorBrewer_1.1-2 oligo_1.28.3
    [15] Biostrings_2.32.1 XVector_0.4.0
    [17] IRanges_1.22.10 oligoClasses_1.26.0
    [19] GEOquery_2.30.1 Biobase_2.24.0
    [21] BiocGenerics_0.10.0

    loaded via a namespace (and not attached):
    [1] affxparser_1.36.0 affyio_1.32.0 bit_1.1-12
    [4] bitops_1.0-6 codetools_0.2-10 ff_2.2-13
    [7] foreach_1.4.2 GenomicRanges_1.16.4 iterators_1.0.7
    [10] preprocessCore_1.26.1 RCurl_1.95-4.5 splines_3.1.1
    [13] stats4_3.1.1 tools_3.1.1 XML_3.98-1.1
    [16] zlibbioc_1.10.0

  11. Reply amiee2406 1月 19,2015 10:45 上午

    欧博士,
    geneCELs<-list.celfiles(full.names=T)
    data.raw <- read.celfiles(geneCELs)
    data.rma <- rma(data.raw, target = "core")
    错误于(function (classes, fdef, mtable) :
    unable to find an inherited method for function ‘probeNames’ for signature ‘"GeneFeatureSet"’
    出现了和楼上一样的错误,请解惑??

    sessionInfo()
    R version 3.1.1 (2014-07-10)
    Platform: x86_64-apple-darwin13.1.0 (64-bit)

    locale:
    [1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8

    attached base packages:
    [1] parallel stats graphics grDevices utils methods base

    other attached packages:
    [1] hugene10sttranscriptcluster.db_8.1.0 hugene10stprobeset.db_8.1.0
    [3] hugene10stv1probe_2.14.0 org.Hs.eg.db_2.14.0
    [5] AnnotationDbi_1.26.1 GenomeInfoDb_1.0.2
    [7] affy_1.42.3 BiocInstaller_1.14.3
    [9] hugene10stv1cdf_2.14.0 pd.hugene.1.0.st.v1_3.8.0
    [11] RSQLite_1.0.0 DBI_0.3.1
    [13] RColorBrewer_1.1-2 oligo_1.28.3
    [15] Biostrings_2.32.1 XVector_0.4.0
    [17] IRanges_1.22.10 oligoClasses_1.26.0
    [19] GEOquery_2.30.1 Biobase_2.24.0
    [21] BiocGenerics_0.10.0

    loaded via a namespace (and not attached):
    [1] affxparser_1.36.0 affyio_1.32.0 bit_1.1-12
    [4] bitops_1.0-6 codetools_0.2-10 ff_2.2-13
    [7] foreach_1.4.2 GenomicRanges_1.16.4 iterators_1.0.7
    [10] preprocessCore_1.26.1 RCurl_1.95-4.5 splines_3.1.1
    [13] stats4_3.1.1 tools_3.1.1 XML_3.98-1.1
    [16] zlibbioc_1.10.0

  12. Reply huangjs 6月 10,2016 2:44 上午

    如何load pd.ragene.1.0.st.v1.

    • Reply admin 6月 13,2016 9:18 上午

      library(pd.ragene.1.0.st.v1)。如果没有安装,就安装一下:library(BiocInstaller); biocLite(“pd.ragene.1.0.st.v1”); library(pd.ragene.1.0.st.v1)

  13. Reply huangjs 6月 10,2016 2:49 上午

    我的错误和上面差不多,您说可以load,但是应该是我方式错了,然后没有成功,请问可以详细一点么?

    > class(AEset)
    [1] “ExpressionFeatureSet”
    attr(,”package”)
    [1] “oligoClasses”
    > qc(AEset)
    Error in (function (classes, fdef, mtable) :
    unable to find an inherited method for function ‘qc’ for signature ‘”ExpressionFeatureSet”’

    > sessionInfo()
    R version 3.3.0 (2016-05-03)
    Platform: i386-w64-mingw32/i386 (32-bit)
    Running under: Windows 7 (build 7601) Service Pack 1

    locale:
    [1] LC_COLLATE=Chinese (Simplified)_People’s Republic of China.936
    [2] LC_CTYPE=Chinese (Simplified)_People’s Republic of China.936
    [3] LC_MONETARY=Chinese (Simplified)_People’s Republic of China.936
    [4] LC_NUMERIC=C
    [5] LC_TIME=Chinese (Simplified)_People’s Republic of China.936

    attached base packages:
    [1] stats4 parallel stats graphics
    [5] grDevices utils datasets methods
    [9] base

    other attached packages:
    [1] oligo_1.36.1
    [2] Biostrings_2.40.2
    [3] XVector_0.12.0
    [4] IRanges_2.6.0
    [5] S4Vectors_0.10.1
    [6] arrayQualityMetrics_3.28.2
    [7] BiocInstaller_1.22.2
    [8] hgu95av2cdf_2.18.0
    [9] simpleaffy_2.48.0
    [10] gcrma_2.44.0
    [11] genefilter_1.54.2
    [12] CLL_1.12.0
    [13] affy_1.50.0
    [14] Biobase_2.32.0
    [15] BiocGenerics_0.18.0
    [16] oligoClasses_1.34.0

    loaded via a namespace (and not attached):
    [1] Rcpp_0.12.5
    [2] Formula_1.2-1
    [3] affxparser_1.44.0
    [4] knitr_1.13
    [5] magrittr_1.5
    [6] cluster_2.0.4
    [7] GenomicRanges_1.24.1
    [8] splines_3.3.0
    [9] zlibbioc_1.18.0
    [10] bit_1.1-12
    [11] xtable_1.8-2
    [12] colorspace_1.2-6
    [13] lattice_0.20-33
    [14] foreach_1.4.3
    [15] latticeExtra_0.6-28
    [16] iterators_1.0.8
    [17] preprocessCore_1.34.0
    [18] setRNG_2013.9-1
    [19] gridSVG_1.5-0
    [20] Matrix_1.2-6
    [21] acepack_1.3-3.3
    [22] limma_3.28.6
    [23] BeadDataPackR_1.24.2
    [24] scales_0.4.0
    [25] Hmisc_3.17-4
    [26] annotate_1.50.0
    [27] AnnotationDbi_1.34.3
    [28] munsell_0.4.3
    [29] affyPLM_1.48.0
    [30] SVGAnnotation_0.93-1
    [31] GenomeInfoDb_1.8.1
    [32] hwriter_1.3.2
    [33] plyr_1.8.4
    [34] stringr_1.0.0
    [35] tools_3.3.0
    [36] base64_2.0
    [37] grid_3.3.0
    [38] nnet_7.3-12
    [39] SummarizedExperiment_1.2.2
    [40] data.table_1.9.6
    [41] gtable_0.2.0
    [42] ff_2.2-13
    [43] beadarray_2.22.2
    [44] DBI_0.4-1
    [45] openssl_0.9.4
    [46] yaml_2.1.13
    [47] survival_2.39-4
    [48] affyio_1.42.0
    [49] RJSONIO_1.3-0
    [50] gridExtra_2.2.1
    [51] ggplot2_2.1.0
    [52] reshape2_1.4.1
    [53] RColorBrewer_1.1-2
    [54] codetools_0.2-14
    [55] rsconnect_0.4.3
    [56] rpart_4.1-10
    [57] RSQLite_1.0.0
    [58] stringi_1.1.1
    [59] XML_3.98-1.4
    [60] vsn_3.40.0
    [61] foreign_0.8-66
    [62] chron_2.3-47
    [63] illuminaio_0.14.0
    [64] Cairo_1.5-9

  14. Reply 生信新手啊 11月 17,2016 10:21 下午

    博主好,这个后边接的limma分析,上边评论里面贴的那个链接失效了。
    所以能不能提供个可供参考的,好知道后边接着limma怎么搞。

  15. Reply puke 11月 27,2017 3:41 上午

    老师你好,按照您的指示,下载了ROOT文件(全是一堆文件,没有安装的执行文件),并解压了,做到biocLite(“xps”,”source=type”),一直发出警告:* installing *source* package ‘xps’ …
    Warning: 运行命令’sh ./configure.win’的状态是127
    ERROR: configuration failed for package ‘xps’
    * removing ‘D:/R-3.4.2/library/xps’
    这是为什么啊???哪里有问题啊

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