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by lckarssen
Wed Aug 03, 2016 10:06 am
Forum: ProbABEL
Topic: Regression analysis on a subset of IDs
Replies: 2
Views: 1526

Re: Regression analysis on a subset of IDs

The --nids option is a bit weird. I never really understood its use. When the option is set (e.g. to a number n ), only the first n individuals will be used. So, apart from only using the first n individuals there is no way to select a subset of individuals. I have added this as an issue in our bug ...
by lckarssen
Wed Jul 27, 2016 4:04 pm
Forum: GenABEL
Topic: P2df / effAB / effBB as NA
Replies: 3
Views: 3292

Re: P2df / effAB / effBB as NA

How many SNPs and how many samples does your analysis have? Do many variants have a low MAF?
by lckarssen
Thu Jun 23, 2016 5:05 pm
Forum: GenABEL
Topic: descriptives.scan how to save output
Replies: 2
Views: 1512

Re: descriptives.scan how to save output

What do you plan to do with the saved data? Is it acceptable if the file is only readable from R? Or should it be, for example, a text file (e.g. a .csv file)?
by lckarssen
Mon Jun 13, 2016 8:38 am
Forum: ProbABEL
Topic: Convert IMPUTE2 into the files that ProbABEL can read
Replies: 1
Views: 1531

Re: Convert IMPUTE2 into the files that ProbABEL can read

Hmm, that's strange. I thought we already squashed that bug a long time ago. Which version of DatABEL are you using? And do you have GenABEL installed? If so, which version?
How many individuals and variants do you have?
by lckarssen
Wed May 04, 2016 9:14 pm
Forum: ProbABEL
Topic: ProbABEL announcements
Replies: 10
Views: 7570

Re: ProbABEL announcements

Dear GenABEL users, Almost one year after the release of v0.4.5, the ProbABEL development team is happy to announce the release of v0.5.0. This release contains several important improvements and fixes and all users are encouraged to upgrade. This release could not have been done without support fro...
by lckarssen
Fri Apr 22, 2016 9:03 pm
Forum: ProbABEL
Topic: Coxph interactions not working (interaction parameter out of [SOLVED]
Replies: 4
Views: 2574

Re: Coxph interactions not working (interaction parameter out of

This problem should be fixed in pull request #26 on Github which will be part of the next ProbABEL release.
by lckarssen
Mon Mar 14, 2016 3:49 pm
Forum: GenABEL
Topic: [SOLVED] Installing GenABEL
Replies: 3
Views: 2464

Re: [SOLVED] Installing GenABEL

Glad it worked out.

About the https vs http thing: I have observed the same. It seems that some CRAN mirrors can be reached via https, while others can't. I guess that all mirrors will transition to https over time.
by lckarssen
Mon Mar 14, 2016 10:51 am
Forum: GenABEL
Topic: [SOLVED] Installing GenABEL
Replies: 3
Views: 2464

Re: Installing GenABEL

The GenABEL package is not part of Bioconductor, it can be found on CRAN (https://cran.r-project.org/web/packages ... index.html). So to install it in R, the following should be sufficient:

Code: Select all

> install.packages("GenABEL")
by lckarssen
Thu Mar 10, 2016 8:54 pm
Forum: ProbABEL
Topic: [SOLVED] Zeros in mlinfo file results in NAN beta and sebeta
Replies: 4
Views: 4190

Re: [SOLVED] Zeros in mlinfo file results in NAN beta and sebeta

Thank for reporting this. The thing is that we use the Rsq column to filter out badly imputed SNPs and simply drop them from the analysis in order to not waste any time on useless computations. So the bug was actually fixed by updating the documentation (although having a look at it now, I could be ...
by lckarssen
Tue Mar 08, 2016 9:52 am
Forum: ProbABEL
Topic: NA and 0 as a values for beta_SNP
Replies: 1
Views: 966

Re: NA and 0 as a values for beta_SNP

What kind of regression are you running? Linear, logistic or CoxPH?
What version of ProbABEL do you use?

Could it be that all your SNPs are rare/have a very low MAF? Please also check the imputation Rsq (both can be found in the info file).

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