Question: error while making a DEGList object on R using edgeR package
0
gravatar for saumya.sharma1509
19 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 • 939 views
ADD COMMENTlink modified 19 months ago by WouterDeCoster44k • written 19 months ago by saumya.sharma15090
1
gravatar for swbarnes2
19 months ago by
swbarnes28.6k
United States
swbarnes28.6k wrote:

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

ADD COMMENTlink written 19 months ago by swbarnes28.6k

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

ADD REPLYlink written 19 months ago by saumya.sharma15090

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

ADD REPLYlink written 19 months ago by WouterDeCoster44k
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 19 months ago by Friederike6.0k
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