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error while making a DEGList object on R using edgeR package

hey, I am doing an RNAseq analysis.(using edgeR) I am loading my data for differential analysis, my data is of normalized gene expression(FPKM). I am now just trying to make DEGList object but, it is showing "NA counts not allowed". I have removed all NA from the data and there is no blank cell in my .csv sheet, it is still showing the error. please suggest what should i do. thank you!!

command -

dgeFull <- DGEList(data, group=sampleInfo$condition) Error: NA counts not allowed

rna-seq edger
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updated by WouterDeCoster WouterDeCoster • written by saumya.sharma1509 • saumya.sharma1509

1 answer

FPKM is not appropriate input for edgeR. You need raw gene counts.

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written by swbarnes2 swbarnes2

thankyou is there any way to convert FPKM data into read counts?

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written by saumya.sharma1509 • saumya.sharma1509

No, not without making assumptions and mistakes. If possible, try to get the original data.

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written by WouterDeCoster WouterDeCoster

original data being fastq files or BAM files, which you could use to generate simple counts of reads overlapping with genes

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written by Friederike Friederike

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