Trouble with DESeqDataSetFromMatrix
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J • 0
@9e1071ba
Last seen 7 weeks ago
United States

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

BiocVersion • 118 views
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@james-w-macdonald-5106
Last seen 1 day ago
United States

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.

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Thanks James, sorry for the missing info. This is actually my first time posting here and did not see the suggestion about putting all the code. Actually, I did start the package but I just realized that the package Biobase needs to be reinstalled

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Also it would help in the future if you tagged the package you were trying to get help on. You tagged BiocVersion which has no impact on your issue. If you had tagged DESeq2 / DESeq the maintainers of those packages would also be notified.

(Hint based on James's answer: Did you do library(DESeq2) ?)

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You are right, again, my fault. yes i did library (DESeq2) I can ask again tagging DEseq2 thanks, Jovanny

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No problem. Just trying to make sure you get the attention of additional people that can help. Cheers

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