geo多晶元差異基因分析時候出現以下錯誤：error in rt[as.vector(diffsig[, 1]), ] :
only 0』s may be mixed with negative subscripts。合併了兩個資料，資料數值都小於10，應該是已經取了log的。但是為什麼會出現這個情況，求大神告知！！！！！！！！
logfoldchange=
1> adjustp=
0.05
>
> library(limma)
> setwd(
"c:\\users\\acer\\desktop\\degs\\07.diff"
)> rt=read.table(
"normalize.txt"
,sep=
"\t"
,header=t,check.names=f)
> rt=as.matrix(rt)
> rownames(rt)
=rt[,1
]> exp=rt[,2
:ncol(rt)
]> dimnames=list(rownames(exp)
,colnames(exp)
)> rt=matrix(as.numeric(as.matrix(exp)
),nrow=nrow(exp)
,dimnames=dimnames)
>
>
#differential
> modtype=c(rep(
"normal",6
),rep(
"endometrium",6
),rep(
"normal",4
),rep(
"endometrium",4
),rep(
"normal",9
),rep(
"endometrium",9
))> design <- model.matrix(~0
+factor(modtype)
)> colnames(design)
<- c(
"con"
,"treat"
)> fit <- lmfit(rt,design)
> cont.matrix<-makecontrasts(treat-con,levels=design)
> fit2 <- contrasts.fit(fit, cont.matrix)
> fit2 <- ebayes(fit2)
>
> alldiff=toptable(fit2,adjust=
'fdr'
,number=
200000
)> write.table(alldiff,file=
"limmatab.xls"
,sep=
"\t"
,quote=f,row.names=f)
>
>
#write table
> diffsig <- alldiff[with(alldiff,
(abs(logfc)
>logfoldchange & adj.p.val < adjustp )),
]> write.table(diffsig,file=
"diff.xls"
,sep=
"\t"
,quote=f,row.names=f)
> diffup <- alldiff[with(alldiff,
(logfc>logfoldchange & adj.p.val < adjustp )),
]> write.table(diffup,file=
"up.xls"
,sep=
"\t"
,quote=f,row.names=f)
> diffdown <- alldiff[with(alldiff,
(logfc<
(-logfoldchange)
& adj.p.val < adjustp )),
]> write.table(diffdown,file=
"down.xls"
,sep=
"\t"
,quote=f,row.names=f)
>
>
#write expression level of diff gene
> hmexp=rt[as.vector(diffsig[,1
]),]
**error in rt[as.vector(diffsig[,1
]),]
: only 0's may be mixed with negative subscripts*
*> diffexp=rbind(id=colnames(hmexp)
,hmexp) 找不到物件
> write.table(diffexp,file=
"diffexp.txt"
,sep=
"\t"
,quote=f,col.names=f) 找不到物件
>
>
#volcano
> pdf(file=
"vol.pdf"
)> xmax=max(
-log10(alldiff$adj.p.val)
)> ymax=max(abs(alldiff$logfc)
)> plot(
-log10(alldiff$adj.p.val)
, alldiff$logfc, xlab=
"-log10(adj.p.val)"
,ylab=
"logfc"
,+ main=
"volcano"
, xlim=c(
0,xmax)
,ylim=c(
-ymax,ymax)
,yaxs=
"i",pch=
20, cex=
0.8)
> diffsub=subset(alldiff, adj.p.vallogfoldchange)
> points(
-log10(diffsub$adj.p.val)
, diffsub$logfc, pch=
20, col=
"red"
,cex=
0.8)
> diffsub=subset(alldiff, adj.p.val(-logfoldchange)
)> points(
-log10(diffsub$adj.p.val)
, diffsub$logfc, pch=
20, col=
"green"
,cex=
0.8)
> abline(h=
0,lty=
2,lwd=3)
> dev.off(
)
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