Thank you for your answer.
However, the output file "transcript differential expression testing" gives the
ratio (log2 of the fold change) of FPKM of a specific transcript between two
conditions, which means this fold change in FPKM does not take the overall gene
expression into consideration (the expression of one gene many be much higher
in condition A than condidtion B) and therefore can not be used as difference
of alternative splicing.
What I am doing is looking for the difference of splicing between two cell
types by examining the output file "splicing differential expression testing".
In this file, column 10 gives the value of "sqrt(JS)" (the explaination of it
is "The splice overloading of the primary transcript, as measured by the square
root of the Jensen-Shannon divergence computed on the relative abundances of
the splice variants", and the value is never larger than 1). My understanding
is that, this value has already taken the overall gene expression into
consideration. But I do not know how much "sqrt(JS)" equals to 2 fold of change
because I want to focus the alternative splicing with 2 fold difference between
two cell types. Do you know how to convert the value of "sqrt(JS)" into "fold"?
In addition, how to understand the sentence "The splice overloading of the
primary transcript"? If one gene have 3 transcript: A, B and C and the
expression of these transcripts is: A=60%, B=25%, and C=15%, do you mean the
primary transcript is A? Does the Cuffdiff take the overall expression
(A+B+C=100%) or just the primary transcript (A=60%) into consideration when
calculates the ratio of transcript B? Actually, it would be much easier for us
if Cuffdiff calculates the ratio of the expression of the alternatively spliced
exon to overall gene expression, and then compare between conditions.
Thanks in advance,
From: Jennifer Jackson [j...@bx.psu.edu]
Sent: Thursday, September 06, 2012 12:38 PM
To: Du, Jianguang
Cc: firstname.lastname@example.org; closetic...@galaxyproject.org
Subject: Re: [galaxy-user] Please help to understand the square root of
Fold is included in the Cuffdiff output. Section "Differential
expression tests", first file, column #9.
Hopefully this helps,
On 9/4/12 1:16 PM, Du, Jianguang wrote:
> Dear All,
> I am looking for the differential splicing events between cell types.
> However the Cuffdiff gives output using "the square root of
> Jensen-shannon divergence" to measure the difference.
> Although I tried my best to understand "the definition of the square
> root of Jensen-shannon divergence", I still could not understand the
> meaning of a specific value of "the square root of Jensen-shannon
> divergence". I would appreciate it very much if anyone let me know how
> to covert "the square root of Jensen-shannon divergence" into "fold".
> For example, how much "the square root of Jensen-shannon divergence" is
> "2 fold difference" equal to.
> Thanks in advance.
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The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at: