Questions tagged [fpkm]

Fragments Per Kilobase per Million. The number of sequenced fragments that align to a specific gene, divided by the length of the gene in kilobases divided by the number of reads in million. It is the number of reads per gene normalised for the gene length and the library size. The term RPKM is an obsolete synonym of FPKM.

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Why use “robust” FPKMs?

Both DESeq2 and edgeR have an FPKM/RPKM function that by default uses normalized library sizes ("robust" option in DESeq2). FPKMs have their own issues, but I thought the main benefit was to ...
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Within and between sample count normalization

recently I came across a situation where RNASeq sample quality was expresses trough DESeq sizeFactor. So authors reported quality of their samples with respect to some publicly available datasets as ...
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What RNA-Seq expression value would be closest to Microarray equivalent?

I know this question may seem strange. I'm using Spearman correlation between gene expression profiles for various reasons (I won't go into details here). As a result, I often compare RNA-Seq and ...
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81 views

In-sample and across samples normalized expression

I want to get the expression data that is in-sample normalized like FPKM and also across samples normalized as obtained using DESeq2 or else. What I am currently doing is that I first normalize the ...
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3k views

How to convert featureCounts to FPKM?

I have seen many posts regarding counts to RPKM and TPM. I haven't seen any post for counts to FPKM. I have RNA-Seq data which is paired-end reads. Extracted the counts using featureCounts for all ...
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How to deal with duplicate genes having different expression values?

I have RNA-Seq data which is FPKM. In the dataframe df first column is gene_name and the ...
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360 views

Spearman correlation between two genes

I have FPKM data for three genes like below: ...
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6k views

How to compute RPKM in R?

I have the following data of fragment counts for each gene in 16 samples: ...
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132 views

Why is FPKM still used for gene expression studies?

Perhaps my understanding is wildly misguided, but I'm seriously confused about why people are still interested using FPKM values for cross sample gene expression analysis. My understanding is, that ...
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321 views

Expression of a gene in different groups

I would like to check the expression of a gene in different groups like Disease vs Normal samples. I want to make a plot out of that to check whether it is significant or not. From this paper lncRNA ...
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3k views

How can I calculate gene_length for RPKM calculation from counts data?

I have read counts data and I want to convert them into RPKM values. For this conversion I need the gene length. Does the gene length need to be calculated based on the sum of coding exonic lengths? ...