Search found 36 matches

by MariaG
Mon May 16, 2011 12:48 pm
Forum: ProbABEL
Topic: [SOLVED] ProbABEL: Compile problem
Replies: 10
Views: 8459

Re: [SOLVED] ProbABEL: Compile problem

hurrah!
by MariaG
Sun May 08, 2011 9:17 pm
Forum: Journal Club on Statistical Genomics
Topic: Bayesian network for learning epistasis
Replies: 0
Views: 4018

Bayesian network for learning epistasis

One approach, and I would say the most common approach, to learn epistasis is “phenotype~genotype” linear models or association tests. The other method is Bayesian network. The fresh paper, I’ve seen on this topic, is “Learning genetic epistasis using Bayesian network scoring criteria”, X. Jiang, R....
by MariaG
Sun May 08, 2011 8:12 pm
Forum: Journal Club on Statistical Genomics
Topic: Notes on GWAS Quality Control/Quality Assurance
Replies: 5
Views: 14247

Re: Notes on GWAS Quality Control/Quality Assurance

Well, the further QC question, for example, is: How important is to check the "normality" of the phenotype? I didn't see any GWAS paper where people would mention the quality of the phenotype.. Even if they use "sqtr" or "log"-transformation they usually don't show the ...
by MariaG
Thu May 05, 2011 8:30 am
Forum: GenABEL
Topic: [SOLVED] merging GenABEL dataframes
Replies: 4
Views: 4160

Re: merging GenABEL dataframes

Thanks Nicola for a good idea!

Actually, I had the same problem. I "solved" it by renaming the colnames after merging.. ;) , e.g. from "sex.x" into "sex"
by MariaG
Thu Apr 21, 2011 6:28 am
Forum: ProbABEL
Topic: [SOLVED] ProbABEL: Compile problem
Replies: 10
Views: 8459

Re: ProbABEL: Compile problem

Hi :)

Where is it possible to download ProbABEL 0.1-9c ?

thanks
by MariaG
Mon Apr 18, 2011 2:35 pm
Forum: ProbABEL
Topic: [Solved] ProbABEL: -nan instead of beta and sebeta
Replies: 2
Views: 2339

Re: ProbABEL: -nan instead of beta and sebeta

Thank you for the reply! The message error: inv file: can not open file makes me think that ProbABEL can't read the inverse sigma matrix file you've entered. Could that be the case? Yes, I try to use the inverse sigma matrix. I'll check one more time, if something wrong with the matrix Look forward ...
by MariaG
Sun Apr 17, 2011 9:59 pm
Forum: Journal Club on Statistical Genomics
Topic: Notes on GWAS Quality Control/Quality Assurance
Replies: 5
Views: 14247

Notes on GWAS Quality Control/Quality Assurance

While doing the Association analysis, e.g. by use of GenaBEL, I was wandered how do people choose the appropriate methods and the parameters’ values for the Quality Control, and how to check the Quality assurance afterwards? Here I provide some links which were useful for me. I’m pretty sure you mig...
by MariaG
Fri Apr 15, 2011 3:04 pm
Forum: ProbABEL
Topic: [Solved] ProbABEL: -nan instead of beta and sebeta
Replies: 2
Views: 2339

[Solved] ProbABEL: -nan instead of beta and sebeta

Hi :) While running ProbABEL v. 0.1-3 (Nov 11, 2009) on imputed data, I've got -nan instead of beta and sebeta for all snps. Also I've an error message: error: inv file: can not open file , but anyway analysis was done: Analysis: 100.00 ... done What -nan means in this case? Is there any problem wit...
by MariaG
Fri Apr 15, 2011 2:35 pm
Forum: ProbABEL
Topic: [SOLVED] ProbABEL: Compile problem
Replies: 10
Views: 8459

Re: [SOLVED] ProbABEL: Compile problem

Dear all, so is the working version already available? Today I downloaded the ProbABEL 0.1-9d and I couldn't compile on it Ubuntu because of the error discussed above... I also tried to download frerror.h and frerror.cpp from r-forge.r-project.org, as it was suggested, hovewer during the compilation...
by MariaG
Thu Apr 14, 2011 1:37 pm
Forum: ProbABEL
Topic: [Solved] ProbABEL: Where to find the "getIDS.pl" ?
Replies: 1
Views: 1824

[Solved] ProbABEL: Where to find the "getIDS.pl" ?

Hi :)

In ProbABEL the example file "prepare_data.R" says:

Code: Select all

 # IDs present in mldose file (in mldoes file order)
 normally generated with getIDS.pl


However I didn't find the getIDS.pl in the ProbABLE folder...
How could I get the getIDS.pl?

Thank you

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