Search found 16 matches

by wuttke
Fri Jun 05, 2015 11:28 am
Forum: ProbABEL
Topic: [SOLVED] ProbABEL: Which allele is the effective allele?
Replies: 2
Views: 2142

Re: ProbABEL: Which allele is the effective allele?

Hi,

I think I solved it by myself.
The perl script I used to convert from Impute2 to (ml)dose format calculates the dosage of A2 instead of A1.
This caused the confusion.

Matthias
by wuttke
Fri Jun 05, 2015 10:09 am
Forum: ProbABEL
Topic: [SOLVED] ProbABEL: Which allele is the effective allele?
Replies: 2
Views: 2142

[SOLVED] ProbABEL: Which allele is the effective allele?

Hi! The ProbABEL manual states on page 15 that the A1 allele is the predictor allele. Now it seems to me the predictor allele frequency given in column 9 of the output is my minor allele frequency, and for the SNP in question A2 is the minor allele. May it be that the manual is wrong and A2 is the p...
by wuttke
Mon Jun 23, 2014 9:51 am
Forum: ProbABEL
Topic: pacoxph - beta may be infinite
Replies: 36
Views: 13992

Re: pacoxph - beta may be infinite

Good news: For my data, now it seems to work perfectly! Both with pacoxph and R, I get exactly the same values and the same NaNs. Thanks a lot!
Matthias
by wuttke
Mon Jun 23, 2014 9:36 am
Forum: ProbABEL
Topic: pacoxph - beta may be infinite
Replies: 36
Views: 13992

Re: pacoxph - beta may be infinite

Hi, I removed the comments that suppress the NAN output and run the old and the new pacoxph version on my data. These are the results: wuttke@imbi7:20140623-TTE-Probabel-Tests$ grep "nan nan nan" chr22_new.out_add.out.txt | wc -l 12130 wuttke@imbi7:20140623-TTE-Probabel-Tests$ grep "n...
by wuttke
Mon Jun 23, 2014 9:16 am
Forum: ProbABEL
Topic: pacoxph - beta may be infinite
Replies: 36
Views: 13992

Re: pacoxph - beta may be infinite

wuttke wrote:.../ProbABEL-v0.4.3-coxfix/ProbABEL$ automake


Well, better to read the documentation before posting...

Code: Select all

autoreconf -i
does the job perfectly.

Sorry for bothering you, best regards, Matthias
by wuttke
Mon Jun 23, 2014 8:11 am
Forum: ProbABEL
Topic: pacoxph - beta may be infinite
Replies: 36
Views: 13992

Re: pacoxph - beta may be infinite

Hi, I checked out the branch, but unfortunately, I've got build problems. .../ProbABEL-v0.4.3-coxfix/ProbABEL$ automake configure.ac: no proper invocation of AM_INIT_AUTOMAKE was found. configure.ac: You should verify that configure.ac invokes AM_INIT_AUTOMAKE, configure.ac: that aclocal.m4 is prese...
by wuttke
Thu Jun 19, 2014 12:27 pm
Forum: ProbABEL
Topic: pacoxph - beta may be infinite
Replies: 36
Views: 13992

Re: pacoxph - beta may be infinite

Hi,

sorry for not coming back to you earlier. I've been on holidays.
Thank you very much for your changes, they are highly appreciated.
I'll give the new version a try in the next days.

Best regards, Matthias
by wuttke
Fri May 16, 2014 1:54 pm
Forum: ProbABEL
Topic: pacoxph - beta may be infinite
Replies: 36
Views: 13992

Re: pacoxph - beta may be infinite

Thank you very much for your answer. I also thought it might be possible the R code has changed in the meantime. coxph.control(eps = 1e-09, toler.chol = .Machine$double.eps^0.75, iter.max = 20, toler.inf = sqrt(eps), outer.max = 10) It seems eps is now 1e-9 (not 1e-8), and they don't check norm(), b...
by wuttke
Thu May 15, 2014 10:37 am
Forum: ProbABEL
Topic: pacoxph - beta may be infinite
Replies: 36
Views: 13992

Re: pacoxph - beta may be infinite

The problem seems to be in this region (coxph_data.cpp:486): VectorXd ueigen = u.data; MatrixXd imateigen = imat.data; VectorXd infs = ueigen.transpose() * imateigen; VectorXd betaeigen = beta.data; if ( infs.norm() > eps || infs.norm() > sqrt(eps) * betaeigen.norm() ) { cerr << "Warning for &q...
by wuttke
Wed May 14, 2014 1:02 pm
Forum: ProbABEL
Topic: pacoxph - beta may be infinite
Replies: 36
Views: 13992

Re: pacoxph - beta may be infinite

I tried v0.4.0, v0.4.1, v0.4.2 and v0.4.3. v0.4.0 and v0.4.1 give a segmentation fault on our cluster, v0.4.2 produces exactly the same output file as v0.4.3. Here is a SNP that does not work at all: rs147996299 G A -1 -1 -1 1 262 0.133489 22 17055978 nan nan nan (As you can see, the allele frequenc...

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