Hi, this code is not running to generate a volcano plot. So what should I do?
GSE51674_series_matrix_txt[,c("ID_REF","GSM1581506","GSM1581507","GSM1581508","GSM1581509")]
View(Control)
Control_mean<-rowMeans(Filter(is.numeric, Control))
Control$Control_mean<-Control_mean
DN<-
GSE51674_series_matrix_txt[,c("ID_REF","GSM1581510", "GSM1581511", "GSM1581512", "GSM1581513", "GSM1581514", "GSM1581517")]
View(DN)
DN_mean<-rowMeans(Filter(is.numeric, DN))
DN$DN_mean<-DN_mean
#Filtering out data for Control(0) and DN(1)
gsmsA<-
"0000111111XXXXXX"
smlA<-strsplit(gsmsA, split="")[[1]]
View(smlA)
selA<- which(smlA !="X")
smlA<- smlA[selA]
gseA<- gse[, selA]
View(gseA)
#DEGs Identification for Group A (control vs DL)
gsA <- factor(smlA)
groupsA<- make.names(c("Control","DN"))
levels(gsA)<- groupsA
gseA$group<- gsA
designA<- model.matrix(~group + 0,gseA)
View(designA)
colnames(designA)<- levels(gsA)
View(designA)
fitA<- lmFit(gseA, designA)
View(fitA)
ctsA<- paste(groupsA[1], groupsA[2], sep="-")
cont.matrixA<- makeContrasts(contrasts = ctsA, levels=designA)
fit2A<- contrasts.fit(fitA, cont.matrixA)
View(cont.matrixA)
View(fit2A)
fit2A<- limma::eBayes(fit2A)
limma::topTable(fit2A)
resultsA<- limma::decideTests(fit2A)
summary(resultsA)
limma::topTable(fit2A)
full_resultsA<- limma::topTable(fit2A, number=Inf)
full_resultsA<- tibble::rownames_to_column(full_resultsA,"ID1")
summary(full_resultsA)
full_resultsA$expression = ifelse(full_resultsA$P.Value <= 0.05 & abs(full_resultsA$logFC)>=1, ifelse(full_resultsA$logFC>1,'Up','Down'), 'Insignificant')
#Volcano plot generation for group A
mycolors<- c("blue","grey","red")
names(mycolors)<- c("Down", "Insignificant", "Up")
vol_plotA<-
ggplot(data=full_resultsA, aes(x=logFC, y=-log10(P.Value), color=expression, label=GENE_SYMBOL)) +
geom_point(alpha=0.4, size=3.5) + geom_text_repel(data=full_resultsA %>% filter(expression == "Down"), hjust=2, min.segment.length=0, max.overlaps=Inf, size=5) +
geom_text_repel(data=full_resultsA %>% filter(expression == "Up"), hjust=-2, min.segment.length=0, max.overlaps=Inf, size=5) +
scale_color_manual(values=mycolors) +
xlim(c(-4.5,4.5)) +
geom_vline(xintercept=c(-1,1),lty=4,col="black",lwd=0.8) +
geom_hline(yintercept=1.301, lty=4, col="black", lwd=0.8) +
labs(x="log2(Fold change)", y="-log10(P-value)", title="Differential expression") +
theme_bw() +
theme(plot.title=element_text(hjust=0.5), legend.position="right", legend.title=element_blank())
vol_plotA
separationA<-as_tibble(full_resultsA)
data_up<-separationA %>% filter(full_resultsA['expression']=="Up")
View(data_upA)
data_downA<- separationA %>% filter(full_resultsA['expression']=="Down")
View(data_downA)
Error in geom_point()
:
! Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in FUN()
:
! object 'GENE_SYMBOL' not found
Run rlang::last_error()
to see where the error occurred.