Software for statistical computing

S

satimis

Hi folks,


I'm prepared to learn SAS Statistical Analysis
http://www.sas.com/technologies/analytics/statistics/stat/index.html

for analysis and reporting of pharmaceutical data. But SAS is NOT free. Are there similar statistical software from Open Source which can be download for use without licence fees. R-Project is great. But it seems NOT for pharmaceutical application. Please advise. TIA

Are there forum specific on statistical computing?


B.R.
satimis
 
I'm a graduate student in stats and have used R a fair bit. I'm just curious what R is lacking that SAS has for "pharmaceutical application"?
 
satimis said:
Hi folks,


I'm prepared to learn SAS Statistical Analysis
http://www.sas.com/technologies/analytics/statistics/stat/index.html

for analysis and reporting of pharmaceutical data. But SAS is NOT free. Are there similar statistical software from Open Source which can be download for use without licence fees. R-Project is great. But it seems NOT for pharmaceutical application. Please advise. TIA

Are there forum specific on statistical computing?


B.R.
satimis
Click to expand...

There is SAS for Linux. Maybe someone help you to port for FreeBSD:
http://www.ats.ucla.edu/default.htm
 
satimis said:
Hi folks,


I'm prepared to learn SAS Statistical Analysis
http://www.sas.com/technologies/analytics/statistics/stat/index.html

for analysis and reporting of pharmaceutical data. But SAS is NOT free. Are there similar statistical software from Open Source which can be download for use without licence fees. R-Project is great. But it seems NOT for pharmaceutical application. Please advise. TIA
Click to expand...

Did you study http://cran.r-project.org/web/packages/ and http://www.bioconductor.org/? There are thousands of special packages for R, some of them are 'pharmacological'.

satimis said:
Are there forum specific on statistical computing?

B.R.
satimis
Click to expand...

see several R mailinglists on http://www.r-project.org/mail.html, especially R-help for beginners.
 
Hi folks,

Thanks for your advice.

The European pharmaceutical manufactures use SAS for analysis which has been approved by the regulators. Therefore on their recruitment they stress experience on SAS is the must. They use SAS to program according to specifications: analysis datasets, pooled datasets, tables, listings, and figures for phase I-IV clinical trials and submission activities. On recruitment they stress applicants being experienced on SAS programming re Oncology.

So there is no way for me learning SAS unless paying the expensive licence fee. Unlike SPSS we can run PSPP learning it. Their features and operations are more or less the same.

On SAS (software) wiki
http://en.wikipedia.org/wiki/SAS_(software)

It lists many Open Source equivalent;
ADMB · DAP · gretl · JMulTi · OpenBUGS · PSPP · R · Simfit · SOFA Statistics · XLispStat

I found it difficult learning all of them to find out SAS equivalent.

B.R.
satimis
 
R certainly can do pharmaceutical analyses

There is no point why you shouldn't use R (math/R) for pharmaceutical/medical research. Manufacturers use SAS but not R mostly merely because they never heard of it. Perhaps you may want to demonstrate your regulators or company that R is actually widely used by pharmaceutical and other facilities e.g. FDA. Perhaps your regulators would be interested in this: http://www.r-project.org/doc/R-FDA.pdf and http://www.fda.gov/ohrms/dockets/ac/07/slides/2007-4308s1-05-fda-mele.ppt (done with R).

If it's credentials that your regulators are concerned about (e.g. the possibility of the analysed work being accepted by the journals in the field), here are some recent publications to show them in which their analyses are done with R:

  • Checkley W, West KP Jr, Wise RA, Baldwin MR, Wu L, LeClerq SC, Christian P, Katz J, Tielsch JM, Khatry S and Sommer A. Maternal vitamin A supplementation and lung function in offspring. N Engl J Med. 2010 May 13;362(19):1784-94.
  • Bouabidi A, Rozet E, Fillet M, Ziemons E, Chapuzet E, Mertens B, Klinkenberg R, Ceccato A, Talbi M, Streel B, Bouklouze A, Boulanger B and Hubert P. Critical analysis of several analytical method validation strategies in the framework of the fit for purpose concept. J Chromatogr A. 2010 May 7;1217(19):3180-92.
  • Sherborne AL, Hosking FJ, Prasad RB, Kumar R, Koehler R, Vijayakrishnan J, Papaemmanuil E, Bartram CR, Stanulla M, Schrappe M, Gast A, Dobbins SE, Ma Y, Sheridan E, Taylor M, Kinsey SE, Lightfoot T, Roman E, Irving JA, Allan JM, Moorman AV, Harrison CJ, Tomlinson IP, Richards S, Zimmermann M, Szalai C, Semsei AF, Erdelyi DJ, Krajinovic M, Sinnett D, Healy J, Gonzalez Neira A, Kawamata N, Ogawa S, Koeffler HP, Hemminki K, Greaves M and Houlston RS. Nat Genet. 2010 Jun;42(6):492-4.
  • Degiuli M, Sasako M, Ponti A; Italian Gastric Cancer Study Group. Morbidity and mortality in the Italian Gastric Cancer Study Group randomized clinical trial of D1 versus D2 resection for gastric cancer. Br J Surg. 2010 May;97(5):643-9.
  • Lucas GM, Chaudhry A, Hsu J, Woodson T, Lau B, Olsen Y, Keruly JC, Fiellin DA, Finkelstein R, Barditch-Crovo P, Cook K and Moore RD. Clinic-based treatment of opioid-dependent HIV-infected patients versus referral to an opioid treatment program: A randomized trial. Ann Intern Med. 2010 Jun 1;152(11):704-11.
  • Li Y, Zou L, Li Q, Haibe-Kains B, Tian R, Li Y, Desmedt C, Sotiriou C, Szallasi Z, Iglehart JD, Richardson AL and Wang ZC. Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer. Nat Med. 2010 Feb;16(2):214-8.
  • Wilkerson MD, Yin X, Hoadley KA, Liu Y, Hayward MC, Cabanski CR, Muldrew KL, Miller CR, Randell SH, Socinski MA, Parsons AM, Funkhouser WK, Lee CB, Robert PJ, Thorne L, Bernard PS, Perou CM and Hayes DN. Lung squamous cell carcinoma mRNA expression subtypes are reproducible, clinically-important and correspond to different normal cell types. Clin Cancer Res. 2010 Jul 19. [Epub ahead of print]
 
Hi semin,


Thanks for your advice and urls.

I have been googling some times on statistics software before reply. R is quite popular having many threads and video on Internet. I'm prepared to have a go on R. Could you please shed me some light on following points;


To use R in profession:-

1) Which OS shall I install/run R? I have VMs running Windows/Linux OS on Oracle VirtualBox. I can install R on any of them. On searching I found most R running on Windows.

2) If installing R on Linux/Unix which version will be more suitable? On desktop or on server with command line operation only?

3) Which category/topic on R I should pay more attention to in respect of medical/pharmaceutical business?


I browsed PubMed.gov
http://www.ncbi.nlm.nih.gov/pubmed

to find your articles. Is there any additional website?

B.R.
satimis
 
Hi satimis,

satimis said:
To use R in profession:-

1) Which OS shall I install/run R? I have VMs running Windows/Linux OS on Oracle VirtualBox. I can install R on any of them. On searching I found most R running on Windows.
Click to expand...

Any version shall be fine. R can be installed on Windows/FreeBSD/Linux/Mac. You see many R running on Windows because many end users use Windows, but that does not mean Windows is the best OS to run R.

2) If installing R on Linux/Unix which version will be more suitable? On desktop or on server with command line operation only?
Click to expand...

It does not really matter. R is a CLI based statistical environment and this is similar to SAS. Although R does have some additional GUI package that helps user get used to some function (e.g. R Commander, TinR, Jagger, etc), in the long run command line is the way to unleash its potential.

In R you will need to write/edit your code. Whereas there are many text editors around, I STRONGLY recommend Emacs (you can find in the ports: editors/emacs) + ESS ("Emacs Speaks Statistics") even though the learning curve of Emacs is somewhat steep. But once you get familiar with Emacs and ESS, your efficiency will be largely improved. (Besides, you can also use Emacs+ESS to write/edit SAS code).

3) Which category/topic on R I should pay more attention to in respect of medical/pharmaceutical business?
Click to expand...

This really depends on what exactly you are going to do. Further detailed info would help me give you some advice.

I browsed PubMed.gov
http://www.ncbi.nlm.nih.gov/pubmed

to find your articles. Is there any additional website?
Click to expand...

PubMed or Medline is usually the first choice. Whilst most database/journals need subscription, there exist some "Open Access" databases/journals that are open to the public to access with no cost (e.g. BMC series). Your medical company should have some info regarding the database/journals associated with your field. (But I wonder why you are looking for these articles since the list was just to show you that many research works done with R have been published in big-name pharmaceutical/medical journals.)

Since your company have also been using SAS, the following books might be of some interest to you:

  • Muenchen, Robert A. (2008) R for SAS and SPSS Users. Springer; 1st ed. ISBN-10: 0387094172
  • Kleinman, Ken and Horton, Nicholas J. (2009) SAS and R: Data Management, Statistical Analysis, and Graphics. Chapman & Hall; 1st ed. ISBN-10: 1420070576
 
semin said:
Hi satimis,



Any version shall be fine. R can be installed on Windows/FreeBSD/Linux/Mac. You see many R running on Windows because many end users use Windows, but that does not mean Windows is the best OS to run R.



It does not really matter. R is a CLI based statistical environment and this is similar to SAS. Although R does have some additional GUI package that helps user get used to some function (e.g. R Commander, TinR, Jagger, etc), in the long run command line is the way to unleash its potential.

In R you will need to write/edit your code. Whereas there are many text editors around, I STRONGLY recommend Emacs (you can find in the ports: editors/emacs) + ESS ("Emacs Speaks Statistics") even though the learning curve of Emacs is somewhat steep. But once you get familiar with Emacs and ESS, your efficiency will be largely improved. (Besides, you can also use Emacs+ESS to write/edit SAS code).



This really depends on what exactly you are going to do. Further detailed info would help me give you some advice.



PubMed or Medline is usually the first choice. Whilst most database/journals need subscription, there exist some "Open Access" databases/journals that are open to the public to access with no cost (e.g. BMC series). Your medical company should have some info regarding the database/journals associated with your field. (But I wonder why you are looking for these articles since the list was just to show you that many research works done with R have been published in big-name pharmaceutical/medical journals.)

Since your company have also been using SAS, the following books might be of some interest to you:

  • Muenchen, Robert A. (2008) R for SAS and SPSS Users. Springer; 1st ed. ISBN-10: 0387094172
  • Kleinman, Ken and Horton, Nicholas J. (2009) SAS and R: Data Management, Statistical Analysis, and Graphics. Chapman & Hall; 1st ed. ISBN-10: 1420070576
Click to expand...

Hi semin,


Thanks for your further advice.

I have R running here for couple days. Actually there is NOT much difference running R on FreeBSD/Linux/Windows, just with command lines on console/terminal. Most the time I run R on Win7 because most manual/tutorials are taught on Windows.(R is running on VM(guest) of Oracle VBox) To learn the basic commands/language is NOT too complicate. But I'm interested to learn using R on anova/t-test etc for pharma industry. Where can I find the sample data making such tests? I did heavy googling when I have spare time. Although the work is hard, it is quite interesting.

The help mailing list of R has very heavy traffic. Most users are running Windows


I used Emacs before but never together with ESS. I'll try installing Emacs+ESS on Win7.


I found following links

Emacs
Installing Emacs on Windows 95/98/2K/NT/ME/XP/Vista/Windows 7
http://www.claremontmckenna.edu/math/alee/emacs/emacs.html


ESS
ESS - Latest Released Version
http://ess.r-project.org/index.php?Section=download

2.2 Microsoft Windows installation
http://www.xemacs.org/Documentation/packages/html/ess_2.html#SEC10


B.R.
satimis
 
Moved to Off-Topic with the same thread title

I have moved the subsequent thread to Off-Topic as this is now less associated with FreeBSD ports and packages.
 
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