extremely small value on cuffnorm fpkm table

Hi, all,

I got some weird values in genes.fpkm_table after cuffnorm. They are really small like "2.88416e-271", "8.78893e-260" "8.89433e-194", there are many in my data, so I'm wondering is this normal to get for fpkm? Any idea what's wrong?

Thanks for the help!

Best,
Ellie

rna-seq normalized-value cufflinks fpkm

• 1,334 views • link

updated 3.9 years ago by Ram

• written 10.8 years ago by Jingyue •

0 answers

No answers yet.

More posts like this

Strange peaks in normalized FPKM data
written 2.1 years ago by Cathy •

Hi! This is my first time asking a question on this forum. My apologies for any (obvious) mistakes. Background: Gene expression data in FPKM format …
best practice for applying FDR to highly similar group DEG analysis
written 4.8 years ago by hs960201 •

hi, i am grad student who is mid of master's degree. one of my project is revealing some genes that differentially expressed between cancer that …
Sample clustering from TCGA dataset
written 8.8 years ago by bharata1803

Hello all, I want to ask for your opinion. First of all I will explain my problem. I have around ~1000 genes of interest and …
StringTie reports 0 coverage for all reference transcripts
written 9.2 years ago by PoGibas

I have used StringTie on mice RNA-seq data. StringTie was run with parameters given in [Nature paper](http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html). Reference gtf annotation was downloaded from the Gencode …
Using ComBat on RNASeq FPKM counts
written 9.8 years ago by ebrudermanver

I want to apply ComBat function in the sva package to an RNA-Seq dataset containing FPKM values. I first added 1 to all counts and …
80% of FPKM values are zero after cufflinks
written 10.4 years ago by haipingl •

I can map all the RNA-seq reads on the chromosome, but after cufflinks process, most of the FPKM values are zero. for example, there is …
Cuffnorm: FPKM values of Genes also appearing among isoforms (but with different value)
written 10.6 years ago by Tobias

When I am running cuffnorm (from cufflinks) on some RNA-Seq BAM files with the GENCODE v19 annotation, I do get out several outputs, most notably …
Running Cuffmerge error "duplicate/invalid 'transcript' "
written 11.0 years ago by Jingyue •

Hi, all, I use cuffmerge after tophat2 & cufflinks for all the transcripts.gtf files, there is an issue shows up: ``` [12:50:00] Loading reference annotation. …
Advice on RNASeq analysis without biological replicates for differential gene expression.
written 11.7 years ago by Christos Gekas •

Hi everybody, I've been lurking for a month learning about RNASeq analysis but now it's time to post my first question! Very briefly I have …
Comparing FPKM values from cufflinks and cuffnorm
written 11.9 years ago by bow

I am trying to calculate an expression value that are comparable in one sample (so I can compare gene A, gene B, etc in the …