Question: error while making a DEGList object on R using edgeR package
0
gravatar for saumya.sharma1509
4 months ago by
saumya.sharma15090 wrote:

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

edger rna-seq • 331 views
ADD COMMENTlink modified 4 months ago by WouterDeCoster39k • written 4 months ago by saumya.sharma15090
1
gravatar for swbarnes2
4 months ago by
swbarnes25.8k
United States
swbarnes25.8k wrote:

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

ADD COMMENTlink written 4 months ago by swbarnes25.8k

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

ADD REPLYlink written 4 months ago by saumya.sharma15090

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

ADD REPLYlink written 4 months ago by WouterDeCoster39k
1

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

ADD REPLYlink written 4 months ago by Friederike4.3k
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