That worked indeed thank you!
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DGElist Ensembl ID recognized as NA values
Hi, I am quite new to R and I am analysing RNA seq data. This is the format of my data frame
transcript_id C1 C2 C3 B4 B5 B6 E4 E5 E6
ENSG00000000003 2019 1619 1597 1343 1026 1010 871 1164 1115
ENSG00000000005 1 2 1 1 1 2 0 0 0
ENSG00000000419 1936 1469 1769 2604 2244 2132 2301 2332 2184
ENSG00000000457 790 826 858 693 561 489 456 615 533
ENSG00000000460 320 372 362 368 285 282 254 342 265
When I use the command data <- DGEList(counts) I get the error Error: NA counts not allowed. I realize that is is beacause of the transcript_id column, because when I remove it it works fine. Any suggestions? Thank you
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h.mon
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1 answer
The problem is edgeR wants a matrix consisting only of integer counts, with the gene identifiers as row names, and sample identifiers as column names. So first assign the trancript_id column to the matrix row names, then remove this column:
rownames(counts) <- counts[ ,1]
counts <- counts[ , -1]
data <- DGEList(counts)
As it is, your counts object holds numbers and strings, so edgerR assigns NAs to the strings.
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it is a bit hard to understand how your R object looks, can you try to reformat your question? when getting errors about NAs in R it is often about values missing from the input, not the format of them (unless it expects a numerical and gets a character)
Problem solved it was due to the character values of the first columns! Thank you.