This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Error in R: DGEList(counts, group) : 'lib.size' must be numeric

I have also asked this question on stackoverflow: https://stackoverflow.com/q/64187464/14385969

Basically I am a student in a Bioinformatics class that is using R to determine the top 10 differentiated genes and construct a heatmap of our preffered dataset. From the GEO database I chose GSE117588. Our prof spoon-feeds us code to punch into R, and I run into trouble when inputting the following command: 

group <- c(rep("G1",3), rep("G2",3))
counts <- data1
cds <- DGEList( counts , group)
names(cds)

head(cds$counts) # original count matrix
cds$samples # contains a summary of your samples
sum(cds$all.zeros) # How many genes have 0 counts across all samples 

cds <- calcNormFactors(cds, method="upperquartile")
cds$samples

In response to cds <- DGEList( counts , group) it returns error message 'lib.size' must be numeric. I have downloaded edgeR and am not sure what to input to debug. I have tried to troubleshoot with a similar question here wherein you add row.names=1 to offset the problems R has with the geneID's (which I'm assuming are the non-numeric part of my dataset it is having trouble with). Please let me know! I'm new to bioinformatics and coding and am eager to learn how to solve and troubleshoot my assignments better.

r r edger
• 2,116 views • link
updated by Biostar Biostar • written by lizzyloo99 • lizzyloo99

Output of head(counts)? I guess that there is a column somewhere with characters.

• 0 views • link
written by ATpoint ATpoint

Start by examining the counts object with head( counts ). The counts object should be a matrix of read counts, that is, it should contain only integer numbers.

edit: to be precise about my comment above, edgeR does accept non-integer numbers, however, they should still be estimates of the counts, to still contain correct information about library sizes. So, for example, one can use the estimated counts from salmon - tximport workflow, but you should not use TPM values, or normalized counts.

• 0 views • link
written by h.mon h.mon

Hello lizzyloo99!

We believe that this post does not fit the main topic of this site.

OP did not follow-up. Please comment if this is still of interest.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 0 views • link
written by ATpoint ATpoint

0 answers

No answers yet.

Log in to answer this question.

More posts like this