[R] RNA Seq Analysis in R

[Jeff Newmiller]

https://www.bioconductor.org/help/

On August 1, 2020 4:01:08 AM PDT, Anas Jamshed <anasjamshed1994 using gmail.com> wrote:
>I choose microarray data GSE75693 of 30 patients with stable kidney
>transplantation and 15 with BKVN to identify differentially expressed
>genes
>(DEGs). I performed this in GEO2R and find R script there and Runs R
>script
>Successfully on R studio as well. The R script is :
>
> # Differential expression analysis with limma
>
>library(Biobase)
>library(GEOquery)
>library(limma)
># load series and platform data from GEO
>
>gset <- getGEO("GSE75693", GSEMatrix =TRUE, AnnotGPL=TRUE)if
>(length(gset) > 1) idx <- grep("GPL570", attr(gset, "names")) else idx
><- 1
>gset <- gset[[idx]]
># make proper column names to match toptable
>fvarLabels(gset) <- make.names(fvarLabels(gset))
># group names for all samples
>gsms <- paste0("000000000000000000000000000000XXXXXXXXXXXXXXX11111",
>        "1111111111XXXXXXXXXXXXXXXXXXX")
>sml <- c()for (i in 1:nchar(gsms)) { sml[i] <- substr(gsms,i,i) }
># eliminate samples marked as "X"
>sel <- which(sml != "X")
>sml <- sml[sel]
>gset <- gset[ ,sel]
># log2 transform
>exprs(gset) <- log2(exprs(gset))
># set up the data and proceed with analysis
>sml <- paste("G", sml, sep="")    # set group names
>fl <- as.factor(sml)
>gset$description <- fl
>design <- model.matrix(~ description + 0, gset)
>colnames(design) <- levels(fl)
>fit <- lmFit(gset, design)
>cont.matrix <- makeContrasts(G1-G0, levels=design)
>fit2 <- contrasts.fit(fit, cont.matrix)
>fit2 <- eBayes(fit2, 0.01)
>tT <- topTable(fit2, adjust="fdr", sort.by="B", number=1250)
>
>tT <- subset(tT,
>select=c("ID","adj.P.Val","P.Value","t","B","logFC","Gene.symbol","Gene.title"))
>DEGs = subset(tT, P.Value < 0.01 & abs(logFC) > 2)
>
>After running this no genes are found plz help me
>
>	[[alternative HTML version deleted]]
>
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-- 
Sent from my phone. Please excuse my brevity.