> source(“http://Bioconductor.org/biocLite.R”)
> biocLite(“limma”)
> library(limma)
> biocLite(“affy”)
> library(affy)
载入需要的程辑包：BiocGenerics
载入需要的程辑包：parallel
载入程辑包：‘BiocGenerics’
下列对象被屏蔽了from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
下列对象被屏蔽了from ‘package:limma’:
plotMA
下列对象被屏蔽了from ‘package:stats’:
xtabs
下列对象被屏蔽了from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind,
colnames, do.call, duplicated, eval, evalq, Filter, Find, get,
intersect, is.unsorted, lapply, Map, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unlist
载入需要的程辑包：Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> affybatch<-ReadAffy(celfile.path="D:\\data\\shiyan\\TB\\tb")
> tb <- expresso(affybatch,bgcorrect.method="rma",normalize.method="constant",pmcorrect.method="pmonly",summary.method="avgdiff")
background correction: rma
normalization: constant
PM/MM correction : pmonly
expression values: avgdiff
background correcting...
done.
normalizing...done.
54675 ids to be processed
| |
|####################|
警告信息：
1: replacing previous import by ‘utils::head’ when loading ‘hgu133plus2cdf’
2: replacing previous import by ‘utils::tail’ when loading ‘hgu133plus2cdf’
> disease<-read.table("D:\\data\\shiyan\\TB\\tbdisease.txt",header=T)
> disease
design TALL BALL
1 GSM336974 1 0
2 GSM336975 1 0
3 GSM336976 1 0
4 GSM336977 1 0
5 GSM336978 1 0
6 GSM336979 1 0
7 GSM336980 1 0
8 GSM336981 1 0
9 GSM336982 1 0
10 GSM336983 1 0
11 GSM337071 0 1
12 GSM337072 0 1
13 GSM337073 0 1
14 GSM337074 0 1
15 GSM337075 0 1
16 GSM337076 0 1
17 GSM337077 0 1
18 GSM337078 0 1
19 GSM337079 0 1
20 GSM337080 0 1
> eset<-exprs(tb)
> disease<-factor(disease[,”Diseaae”])
> design<-model.matrix(～-1+disease)
> contrast.matrix<-makeContrasts(contrasts=”TALL-BALL”,levels=design)
> fit<-lmFit (eset,design)
错误于as.vector(x, mode) :
cannot coerce type 'closure' to vector of type 'any'
