Search found 36 matches

by MariaG
Fri Feb 15, 2013 4:50 pm
Forum: ProbABEL
Topic: [SOLVED] ProbABEL - pvalue
Replies: 4
Views: 3222

Re: [SOLVED] ProbABEL - pvalue

Dear developers

Would be really nice to have p-values calculated automatically
It was already discussed here:
http://r-forge.r-project.org/tracker/index.php?func=detail&aid=2086&group_id=505&atid=2061

Do you plan to implement it?

best
Maria
by MariaG
Fri Feb 15, 2013 1:47 pm
Forum: GenABEL
Topic: problem with impute2databel() function
Replies: 11
Views: 5908

Re: problem with impute2databel() function

Hi! I've got the same error, while working on MAC today: ERROR in Rstaff:failed in text2fvf_R Index file not exists: /Volumes/Local/home/statistics/GWA/CADASIL/Input/genotypes/C1.chr17selected.databel.txt.fvi Error in checkSlotAssignment(object, name, value) : assignment of an object of class "...
by MariaG
Wed Jan 30, 2013 1:50 pm
Forum: Journal Club on Statistical Genomics
Topic: Mixed-models for GWA
Replies: 2
Views: 5072

Re: Mixed-models for GWA

PS. Unfortunatelly I was not able to upload the corresponding .pdf file.
Do we have any limitations for uploading documents on Forum?
Is it possible to allow uploading .pdf at least here, in Journal Club?

Maria
by MariaG
Wed Jan 30, 2013 1:32 pm
Forum: Journal Club on Statistical Genomics
Topic: Mixed-models for GWA
Replies: 2
Views: 5072

Mixed-models for GWA

Nat Genet. 2012 Jun 17;44(7):821-4. doi: 10.1038/ng.2310. Genome-wide efficient mixed-model analysis for association studies. ( GEMMA ) Zhou X, Stephens M. Department of Human Genetics, University of Chicago, Chicago, Illinois, USA. xz7@uchicago.edu http://www.ncbi.nlm.nih.gov/pubmed/22706312 "...
by MariaG
Wed Jan 30, 2013 12:26 pm
Forum: GenABEL
Topic: [SOLVED] How to?: From birdseed-v2.txt to GenABEL format
Replies: 2
Views: 1204

Re: How to?: From birdseed-v2.txt to GenABEL format

Yurii, thanks for answer :)
I've solved the problem by using Python to rewrite the data format
I just thought that's there is already a common way of doing it ;)
by MariaG
Thu Jan 10, 2013 4:07 pm
Forum: GenABEL
Topic: [SOLVED] Installation/load error
Replies: 17
Views: 5420

Re: Installation/load error

The advise of Nicola worked for me (on MAC) if I use

Package source:GenABEL_1.7-3.tar.gz
from here:
http://cran.at.r-project.org/web/packag ... index.html

but NOT
MacOS X binary:GenABEL_1.7-2.tgz

:)
by MariaG
Thu Jan 10, 2013 2:46 pm
Forum: GenABEL
Topic: [SOLVED] Installation/load error
Replies: 17
Views: 5420

Re: Installation/load error

Hi there,
I have the same problem on MAC...
by MariaG
Tue Dec 04, 2012 2:45 pm
Forum: GenABEL
Topic: [SOLVED] How to?: From birdseed-v2.txt to GenABEL format
Replies: 2
Views: 1204

[SOLVED] How to?: From birdseed-v2.txt to GenABEL format

Hello,

I would very appreciate to know, how do you convert the affymetrix genotypic files (birdseed-v2.txt) into GenABEL/Plink format?

thanks in advance

Maria
by MariaG
Wed Oct 19, 2011 2:52 pm
Forum: GenABEL
Topic: Estimate lambda
Replies: 2
Views: 2680

Re: Estimate lambda

Here is the additional message from the same author (hakosalo): Hi. I have this type of error message appearing over and over again (my data is not human, its canine) "Testassoc<-qtscore(pheno, own.data, trait="binomial") Warning message: In qtscore(pheno, own.data, trait = "bino...
by MariaG
Fri Aug 26, 2011 7:44 am
Forum: Journal Club on Statistical Genomics
Topic: Nature Protocols. Basic statistical analysis in genetic case
Replies: 3
Views: 7209

Nature Protocols. Basic statistical analysis in genetic case

Nature protocols in 2007 – 2011 presented something like a series of papers referred to the protocols for association analysis: [url] http://www.nature.com/search/executeSearch?sp-q=gwa&sp-p=all&include-collections=journals_nature%2Ccrawled_content&exclude-collections=journals_palgrave%2...

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