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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.

3
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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 … mainly used for single-end reads data. Do you think I can use the above function for converting counts to FPKM as my data is paired end? [TCGA data: HTSeq counts are converted to HTSeq FPKM
asked Oct 22 '18 by beginner
2
votes
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I have RNA-Seq data which is FPKM. In the dataframe df first column is gene_name and the other 100 columns are samples. Usually if it is counts data I do like following: df2 <- aggregate … (. ~ gene_name, data = df, max) I'm not sure what do with the FPKM data if there are duplicate genes with different FPKM value for the same sample. Lets say it looks like this: gene_name sample1 …
asked Oct 25 '18 by beginner
4
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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 …
asked May 9 '18 by beginner