[BioC] LPE question

[Jain, Nitin]

Dear Lisa,

The function 'fdr.adjust' uses for loops in R, which are not very efficient.  However, I have tried it on 64-bit Linux machine in Pfizer, and it runs quite fast (< 1 hr) for 1000-iterations. 

LPE is best suited if the number of replicates and samples are less than or equal to 5. We upgraded the LPE package from the original paper (2003), and published a paper in BMC Bioinformatics. The latest version is on Bioconductor since early last year. (http://www.biomedcentral.com/1471-2105/6/187)

Originally, when we collaborated with S-Plus, then there was not the comprehensive 'resampling' based fdr adjustment. I am not aware about whether S-Plus function has been upgraded or not. Also, am not sure if they are using the C-code for the resampling part or the regular S-engine.  I am cc'ing this mail to Dr. Lee in Univ. of Virginia, who can shed more light on this.

To obtain Bonferroni adjusted values, just run lpe test (without fdr.adjust) and obtain "median.diff" and "z.stats" (these values are in the result of lpe function). Then calculate the p-values for each gene:

pnorm.diff <- pnorm(median.diff, mean = 0, sd = std.dev)
p.out <- 2 * apply(cbind(pnorm.diff, 1 - pnorm.diff), 1, min)

and multiply the p-values (p.out) by the number of genes to obtain the Bonferroni adjusted p-values (use pvalue =1, if it is greater than 1).

We will add this option (Bonferroni) in the new version of LPE package.

Best,
Nitin


On 2/15/06, Lisa Croner <Lisa.Croner at biogenidec.com> wrote:
>  
> Hello Dr. Jain, 
> I have been using your LPE Bioconductor package (in R), and find that fdr.adjust with resamp or mix.all is very slow on both my windows and new linux machines.  It appears that a 1000-iteration run may take 16 hours to complete.  On the other hand, a colleague tells me that running fdr.adjust with resamp for 1000 iterations under S-Plus completes in about 5 minutes on his (windows, I believe) laptop.  Does this make sense to you?  Is it know that S-Plus is so much faster than R?  Do you perhaps have a faster version of LPE to run under R? 


> One other question:  How can one run simply the Bonferroni adjusted LPE test from your 2003 Bioinformatics paper (Figure 2 and page 1948), using the LPE R package? 

> Many thanks for further information, 
> Lisa 
>  
> --------------------------------------------------------
>  Lisa J. Croner, Ph.D.
>  Scientist II, Computational Biology
>  Biogen Idec
>  San Diego, CA
>  (858) 401-5669
>  lisa.croner at biogenidec.com
>  --------------------------------------------------------
>   


______________________
Nitin Jain, PhD
<nitin.jain at pfizer.com>
Non Clinical Statistics
Pfizer, Inc. (Groton, CT)
Bldg: 260, # 1451
Ph:  (860) 686-2526 (Office)
Fax: (860) 686-6170

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