Entering edit mode
3 months ago
mounavisirekolam
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0
I have fpkm file which has 24062 gene and their expression values across four conditions. I have a file of list of x_chr genes extracted from gff file which were 2600 when I have performed intersection I got 1005 around and when I have intersected the same file to differential gene expression data x_chr genes were 1032 how is that possible ?
Can you clarify more? So you have extracted certain genes from a GFF and don't find them back in some other file, is that correct? Has the FPKM file been filtered for expression level? That is common.
I am trying to study x-chr dynamics across different harmone conditions. I mean Fpkm file has all genes right? Genes of X_chr extracted from gff file is 2615 approximately but the that 2615 when intersected with fpkm we should get 2615 but I am getting only 964 but ideally speaking 2615 should be there right ? Another question is when these genes of x-chr(2615) intersected with 3 files of differentially expressed genes one of it is 465,but other have 1005 how come 1005 is more than 964.
Nobody can tell without knowing whether the fpkm file has been filtered or is even based on the same annotation as the gff file.
What do u mean by filtered fpkm file ?
I have fpkm table is there a way to tell from which gff was it generated ?
Ask the one who made it. Look, I cannot help you here. You give essentially no details. Talk to the person who made the file. If that is not possible or code to create the file is not available then don't use it. It's unreliable without documented code.