Hi,
I'm trying to calculate p-value to findout definitely expressed genes
compare A to B situation.
I got this data(this is a part of data) from whole organism , and each
number means each expression values (that means, we could think 'a' gene
is 13 in A situation, and it turns 30 in B situation)
To findout probability, I'm going to use Audic - Claverie Method. ( The
significance of digital gene expression profiles. 1997)
But using this equation p(x|y), I have to calculate (x+y)! first. but I
can't calculate (157+221)! or (666+1387)! in R.
That's probabily the handling problem of huge number, How could I
calculate p value in this data with R?
A B
Total 5874641 6295980
a 13 30
b 36 39
c 0 5
d 40 61
e 16 20
f 13 11
g 3 3
h 9 5
i 12 35
j 157 221
k 17 39
l 6 17
m 666 1387
n 2 5
The significance of digital gene expression profiles.
Audic S
<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22A
udic%20S%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Result
sPanel.Pubmed_RVAbstractPlusDrugs1> , Claverie JM
<http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22C
laverie%20JM%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Re
sultsPanel.Pubmed_RVAbstractPlusDrugs1> .
[[alternative HTML version deleted]]
If you want to compute (157+221)! then sum up the log:> a <- 1:(157+221) > sum(log10(a))[1] 811.8165 This is about 6.55e811 which exceeds the range of floating point numbers (1.797693e+308). You might check out the Brobdingnag package. On Feb 18, 2008 6:23 PM, Hyojin Lee <hyojinl at bcgsc.ca> wrote:> Hi, > I'm trying to calculate p-value to findout definitely expressed genes > compare A to B situation. > I got this data(this is a part of data) from whole organism , and each > number means each expression values (that means, we could think 'a' gene > is 13 in A situation, and it turns 30 in B situation) > To findout probability, I'm going to use Audic - Claverie Method. ( The > significance of digital gene expression profiles. 1997) > > But using this equation p(x|y), I have to calculate (x+y)! first. but I > can't calculate (157+221)! or (666+1387)! in R. > That's probabily the handling problem of huge number, How could I > calculate p value in this data with R? > > > A B > Total 5874641 6295980 > a 13 30 > b 36 39 > c 0 5 > d 40 61 > e 16 20 > f 13 11 > g 3 3 > h 9 5 > i 12 35 > j 157 221 > k 17 39 > l 6 17 > m 666 1387 > n 2 5 > > > > > > > > > > The significance of digital gene expression profiles. > > Audic S > <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22A > udic%20S%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Result > sPanel.Pubmed_RVAbstractPlusDrugs1> , Claverie JM > <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22C > laverie%20JM%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Re > sultsPanel.Pubmed_RVAbstractPlusDrugs1> . > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve?
Use lchoose and use logarithms throughout.> x=666 > y=1287 > lchoose(x+y,x)-(x+y)*log(2)[1] -104.4265> Pxy = exp(lchoose(x+y,x)-(x+y)*log(2))[1] 4.447787e-46 Joe -----Original Message----- From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Hyojin Lee Sent: Monday, February 18, 2008 5:23 PM To: r-help at r-project.org Subject: [R] Huge number Hi, I'm trying to calculate p-value to findout definitely expressed genes compare A to B situation. I got this data(this is a part of data) from whole organism , and each number means each expression values (that means, we could think 'a' gene is 13 in A situation, and it turns 30 in B situation) To findout probability, I'm going to use Audic - Claverie Method. ( The significance of digital gene expression profiles. 1997) But using this equation p(x|y), I have to calculate (x+y)! first. but I can't calculate (157+221)! or (666+1387)! in R. That's probabily the handling problem of huge number, How could I calculate p value in this data with R? A B Total 5874641 6295980 a 13 30 b 36 39 c 0 5 d 40 61 e 16 20 f 13 11 g 3 3 h 9 5 i 12 35 j 157 221 k 17 39 l 6 17 m 666 1387 n 2 5 The significance of digital gene expression profiles. Audic S <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22A udic%20S%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Result sPanel.Pubmed_RVAbstractPlusDrugs1> , Claverie JM <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22C laverie%20JM%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Re sultsPanel.Pubmed_RVAbstractPlusDrugs1> . [[alternative HTML version deleted]] ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.