Question: MEDIPS - RPKM
0
gravatar for malbert1
4.1 years ago by
malbert10
Australia
malbert10 wrote:

I was hoping someone could please help explain how RPKM values are calculated using the MEDIPS package?

From the source code (v1.16) it says RPKM values are calculated the following way:

 (genome_count(Set)*10^9)/(window_size*number_regions(Set))

I am assuming that genome_count(Set) is referring to  "number of reads detected in each bin" and that window_size it the bin size. However, I am a bit unsure what number_regions(Set) refers to? Is that the number of windows generated for the reference genome or something else? And how does this compare/deviate from calculating the RPKM values by dividing the genome_count*10^9 with the total read count (sum(genome_count(Set)))

Also, does anyone know whether the strategy for calculating RPKM values has changes between MEDIPS versions (fx. between v1.6 and v1.16)?

Cheers,

Maria

 

 

 

medips • 766 views
ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by malbert10
Answer: MEDIPS - RPKM
1
gravatar for Lukas Chavez
4.1 years ago by
Lukas Chavez510
USA/La Jolla/UCSD
Lukas Chavez510 wrote:
Dear Maria, your interpretations of genome_count(Set) and window_size are correct, but number_regions(Set) is the total number of reads considered for calculating coverage at the genome wide windows (or 'total read count' as you say). It differs from the sum over the counts of all windows, because MEDIPS counts each (extended) read at all window it overlaps (this is done because it is unknown at which position of the enriched DNA fragment the mark is located). MEDIPS version 1.10.0 was a major update where also the way of calculating rpkm values was changed (see also the section ‘Updates' of the MEDIPS vignette). For example, the window size was not considered previously. All the best, Lukas > On 25 Mar 2015, at 15:53, malbert1 [bioc] <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org <https: support.bioconductor.org=""/> > User malbert1 <https: support.bioconductor.org="" u="" 6922=""/> wrote Question: MEDIPS - RPKM <https: support.bioconductor.org="" p="" 66027=""/>: > > > I was hoping someone could please help explain how RPKM values are calculated using the MEDIPS package? > > From the source code (v1.16) it says RPKM values are calculated the following way: > > (genome_count(Set)*10^9)/(window_size*number_regions(Set)) > > I am assuming that genome_count(Set) is referring to "number of reads detected in each bin" and that window_size it the bin size. However, I am a bit unsure what number_regions(Set) refers to? Is that the number of windows generated for the reference genome or something else? And how does this compare/deviate from calculating the RPKM values by dividing the genome_count*10^9 with the total read count (sum(genome_count(Set))) > > Also, does anyone know whether the strategy for calculating RPKM values has changes between MEDIPS versions (fx. between v1.6 and v1.16)? > > Cheers, > > Maria > > > > > > You may reply via email or visit MEDIPS - RPKM >
ADD COMMENTlink written 4.1 years ago by Lukas Chavez510
Answer: MEDIPS - RPKM
0
gravatar for malbert1
4.1 years ago by
malbert10
Australia
malbert10 wrote:

Thanks for your reply Lukas and sorry for the confusion! 

Cheers,

Maria

 

ADD COMMENTlink written 4.1 years ago by malbert10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 143 users visited in the last hour