Hi, I am having a little trouble with R-Studio. It is not finding the function "DESeqDataSetFromMatrix". This is my line of commands:

countdata1 <- read.table("RawCounts_baseline_MRDPos_vs_MRDNeg.txt", row.names=1, header=T, check.names = F)
countdata1 <- as.matrix(countdata1)
storage.mode(countdata1) = "integer"
coldata <- read.table("coldata_baseline_MRDPos_vs_MRDNeg.txt", header=T, row.names=1, sep="\t")
**dds <- DESeqDataSetFromMatrix(countData = countdata1, colData = coldata, design = ~ MRD)**
dds <- dds[rowSums(counts(dds))>1, ]
dds <-estimateSizeFactors(dds)
idx <- rowSums(counts(dds, normalized=TRUE) >=1) >= 35
dds <- dds[idx,]
dds <- DESeq(dds)

I am using R-Studio v1.4.1717 Any suggestions? thanks, Jovanny

It would be better if you cut'n'pasted your actual session results rather than the commands you submitted. Without seeing the R output it's a bit of a mystery. Also, do note that when you start a post, there's this block that says 'Put all your code in this place' which you apparently just deleted and pasted in your code. Ideally you would have followed those instructions so others (me, for instance) wouldn't have to do it for you in order to be able to read your code. If you expect to get far with R, paying attention to what it says on the screen is an invaluable thing to do.

Anyway, I assume that what you actually got was something like

> DESeqDataSetFromMatrix(arguments, go, here)
Error in DESeqDataSetFromMatrix(arguments, go, here) : 
  could not find function "DESeqDataSetFromMatrix"

Which is what R will tell you when you haven't actually loaded the package (DESeq2 in this case) that contains the function.