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pachterlab / kma

Keep Me Around: Intron Retention Detection
GNU General Public License v2.0
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Problem in R: computing dominator #4

Open LiLey opened 8 years ago

LiLey commented 8 years ago

hello I tried to use Kma for the detection of intronretention in my RNA-seq data. Now I have the problem that with my data the dominator is not computed in R, maybe someone knows what might have gone wrong

Thanks in advance!

head(ir$flat) intron sample numerator denominator retention condition unique_counts 1 chr9:130579764-130595482 ortho1 178608.1000 NA NA ortho 2003 2 chr9:130595588-130609953 ortho1 106730.6000 NA NA ortho 1033 3 chr9:130609987-130612455 ortho1 1039.8910 NA NA ortho 2 4 chr9:130612505-130612955 ortho1 0.0000 NA NA ortho 0 5 chr9:130613027-130614287 ortho1 0.0000 NA NA ortho 0 6 chr9:130614345-130616354 ortho1 648.3534 NA NA ortho 1

a1lu commented 8 years ago

This Problem was caused by the fasta file. It seems that there is a problem parsing sequence names like >NP_852610.1 . Without .1 the denominator was calculated (for minimal example just add .1 to a sequence name). Although during hypothesis testing var_retention was always NA and pvalue / qvalue equaled to 1 or 0 (while in the worked example the two values are looking like some float values.).

marykozi commented 2 years ago

Are there any other reasons for problem? Any formats of target_id's values (NP_852610.1, NP_852610, ENSMUST00000166431.9, "ENSMUST00000166431.9") does not change the fact, that the denominator is always NA