Question: gene symbol in r
0
gravatar for miravet65
2.1 years ago by
miravet650
miravet650 wrote:

I am having a problem in getting gene symbol after analysis GEO data.

I can get logFC, P.value but in gene.symbol only show <NA>

gr<-as.factor(gr)
gset$description <- gr
design <- model.matrix(~ description + 0, gset)
colnames(design) <- levels(gr)
fit <- lmFit(gset, design)
cont.matrix <- makeContrasts("cp-np", levels=design)
fit2 <- contrasts.fit(fit, cont.matrix)
fit2 <- eBayes(fit2, 0.01)
tT <- topTable(fit2, adjust="fdr", sort.by="B", number=Inf)

tT <- subset(tT, select=c("adj.P.Val","P.Value","logFC","Gene.symbol"))
write.table(tT, file=stdout(), row.names=F, sep="\t")

Output:

 Gene.symbol
 <NA>
  <NA>
<NA>
 FBXL21
      <NA>
   <NA>
R gene • 1.1k views
ADD COMMENTlink modified 7 months ago by zx87547.1k • written 2.1 years ago by miravet650

I think if you set gene symbols as data frames' rownames, It is not a problem.

ADD REPLYlink written 2.1 years ago by zjhzwang180

This question lacks the required information to answer this. You should at least add some commands you ran, how can we guess what's wrong without?

ADD REPLYlink written 2.1 years ago by WouterDeCoster38k
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