Hello, Can I apply the quantile function qt() this way? qt(pvals/2, 406-34, lower.tail = F) to get the T-scores? Thanks Ama
calculating t-score/t-stats as my zscores
13 messages · Ana Marija, Patrick (Malone Quantitative), Rui Barradas
Hello, That gives the *absolute* t-scores. If it's all you need/want, then the answer is yes, you can. Hope this helps, Rui Barradas ?s 14:28 de 06/05/20, Ana Marija escreveu:
Hello, Can I apply the quantile function qt() this way? qt(pvals/2, 406-34, lower.tail = F) to get the T-scores? Thanks Ama
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Hi Rui, Thank you for getting back to me. Is there is a better way to calculate Z scores if I have p values, SE and Beta? Thanks Ana
On Wed, May 6, 2020 at 9:27 AM Rui Barradas <ruipbarradas at sapo.pt> wrote:
Hello, That gives the *absolute* t-scores. If it's all you need/want, then the answer is yes, you can. Hope this helps, Rui Barradas ?s 14:28 de 06/05/20, Ana Marija escreveu:
Hello, Can I apply the quantile function qt() this way? qt(pvals/2, 406-34, lower.tail = F) to get the T-scores? Thanks Ama
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Hello, Sorry but after reading my answer I believe it's not completely clear. I meant absolute values, the actual t-scores as computed from the data might be negative. Your code will always produce positive numbers. Hope this helps, Rui Barradas ?s 15:27 de 06/05/20, Rui Barradas escreveu:
Hello, That gives the *absolute* t-scores. If it's all you need/want, then the answer is yes, you can. Hope this helps, Rui Barradas ?s 14:28 de 06/05/20, Ana Marija escreveu:
Hello, Can I apply the quantile function qt() this way? qt(pvals/2, 406-34, lower.tail = F) to get the T-scores? Thanks Ama
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
thanks, can you please tell em what would be the way not to get the absolute (always positive values)
On Wed, May 6, 2020 at 9:33 AM Rui Barradas <ruipbarradas at sapo.pt> wrote:
Hello, Sorry but after reading my answer I believe it's not completely clear. I meant absolute values, the actual t-scores as computed from the data might be negative. Your code will always produce positive numbers. Hope this helps, Rui Barradas ?s 15:27 de 06/05/20, Rui Barradas escreveu:
Hello, That gives the *absolute* t-scores. If it's all you need/want, then the answer is yes, you can. Hope this helps, Rui Barradas ?s 14:28 de 06/05/20, Ana Marija escreveu:
Hello, Can I apply the quantile function qt() this way? qt(pvals/2, 406-34, lower.tail = F) to get the T-scores? Thanks Ama
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
I guess I can have z-score=Beta/StdErr
On Wed, May 6, 2020 at 9:37 AM Ana Marija <sokovic.anamarija at gmail.com> wrote:
thanks, can you please tell em what would be the way not to get the absolute (always positive values) On Wed, May 6, 2020 at 9:33 AM Rui Barradas <ruipbarradas at sapo.pt> wrote:
Hello, Sorry but after reading my answer I believe it's not completely clear. I meant absolute values, the actual t-scores as computed from the data might be negative. Your code will always produce positive numbers. Hope this helps, Rui Barradas ?s 15:27 de 06/05/20, Rui Barradas escreveu:
Hello, That gives the *absolute* t-scores. If it's all you need/want, then the answer is yes, you can. Hope this helps, Rui Barradas ?s 14:28 de 06/05/20, Ana Marija escreveu:
Hello, Can I apply the quantile function qt() this way? qt(pvals/2, 406-34, lower.tail = F) to get the T-scores? Thanks Ama
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Hello,
By z-scores do you mean function help('scale')?
Hope this helps,
Rui Barradas
?s 15:31 de 06/05/20, Ana Marija escreveu:
Hi Rui, Thank you for getting back to me. Is there is a better way to calculate Z scores if I have p values, SE and Beta? Thanks Ana On Wed, May 6, 2020 at 9:27 AM Rui Barradas <ruipbarradas at sapo.pt> wrote:
Hello, That gives the *absolute* t-scores. If it's all you need/want, then the answer is yes, you can. Hope this helps, Rui Barradas ?s 14:28 de 06/05/20, Ana Marija escreveu:
Hello, Can I apply the quantile function qt() this way? qt(pvals/2, 406-34, lower.tail = F) to get the T-scores? Thanks Ama
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
as defined here: https://huwenboshi.github.io/data%20management/2017/11/23/tips-for-formatting-gwas-summary-stats.html where Effect size is Beta
On Wed, May 6, 2020 at 9:41 AM Rui Barradas <ruipbarradas at sapo.pt> wrote:
Hello,
By z-scores do you mean function help('scale')?
Hope this helps,
Rui Barradas
?s 15:31 de 06/05/20, Ana Marija escreveu:
Hi Rui, Thank you for getting back to me. Is there is a better way to calculate Z scores if I have p values, SE and Beta? Thanks Ana On Wed, May 6, 2020 at 9:27 AM Rui Barradas <ruipbarradas at sapo.pt> wrote:
Hello, That gives the *absolute* t-scores. If it's all you need/want, then the answer is yes, you can. Hope this helps, Rui Barradas ?s 14:28 de 06/05/20, Ana Marija escreveu:
Hello, Can I apply the quantile function qt() this way? qt(pvals/2, 406-34, lower.tail = F) to get the T-scores? Thanks Ama
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Guessing for Ana, but no, that's a different meaning. Beta/StdErr is a z statistic--a test statistic against (usually) the tails of the unit normal distribution. So like a t-test with infinite df.
On Wed, May 6, 2020 at 10:41 AM Rui Barradas <ruipbarradas at sapo.pt> wrote:
Hello,
By z-scores do you mean function help('scale')?
Hope this helps,
Rui Barradas
?s 15:31 de 06/05/20, Ana Marija escreveu:
Hi Rui, Thank you for getting back to me. Is there is a better way to calculate Z scores if I have p values, SE and Beta? Thanks Ana On Wed, May 6, 2020 at 9:27 AM Rui Barradas <ruipbarradas at sapo.pt> wrote:
Hello, That gives the *absolute* t-scores. If it's all you need/want, then the answer is yes, you can. Hope this helps, Rui Barradas ?s 14:28 de 06/05/20, Ana Marija escreveu:
Hello, Can I apply the quantile function qt() this way? qt(pvals/2, 406-34, lower.tail = F) to get the T-scores? Thanks Ama
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Patrick S. Malone, Ph.D., Malone Quantitative NEW Service Models: http://malonequantitative.com He/Him/His
Thanks Patrick, so in conclusion this is fine? z-score=Beta/StdErr On Wed, May 6, 2020 at 9:52 AM Patrick (Malone Quantitative)
<malone at malonequantitative.com> wrote:
Guessing for Ana, but no, that's a different meaning. Beta/StdErr is a z statistic--a test statistic against (usually) the tails of the unit normal distribution. So like a t-test with infinite df. On Wed, May 6, 2020 at 10:41 AM Rui Barradas <ruipbarradas at sapo.pt> wrote:
Hello,
By z-scores do you mean function help('scale')?
Hope this helps,
Rui Barradas
?s 15:31 de 06/05/20, Ana Marija escreveu:
Hi Rui, Thank you for getting back to me. Is there is a better way to calculate Z scores if I have p values, SE and Beta? Thanks Ana On Wed, May 6, 2020 at 9:27 AM Rui Barradas <ruipbarradas at sapo.pt> wrote:
Hello, That gives the *absolute* t-scores. If it's all you need/want, then the answer is yes, you can. Hope this helps, Rui Barradas ?s 14:28 de 06/05/20, Ana Marija escreveu:
Hello, Can I apply the quantile function qt() this way? qt(pvals/2, 406-34, lower.tail = F) to get the T-scores? Thanks Ama
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
-- Patrick S. Malone, Ph.D., Malone Quantitative NEW Service Models: http://malonequantitative.com He/Him/His
Hello,
You can write a function to compute the scores:
z_score <- function(x, beta = mean, beta0 = 0){
beta <- match.fun(beta)
n <- length(x)
score <- sqrt(n)*(beta(x) - beta0)/sd(x)
names(score) <- if(n < 30) "t.score" else "z.score"
score
}
# data example
x <- rt(20, df = 1)
tt <- t.test(x)
pvals <- tt$p.value
# Now compare these 3 results and see if it answers the question
qt(pvals/2, 19, lower.tail = F)
tt$statistic
z_score(x)
Hope this helps,
Rui Barradas
?s 15:40 de 06/05/20, Ana Marija escreveu:
I guess I can have z-score=Beta/StdErr On Wed, May 6, 2020 at 9:37 AM Ana Marija <sokovic.anamarija at gmail.com> wrote:
thanks, can you please tell em what would be the way not to get the absolute (always positive values) On Wed, May 6, 2020 at 9:33 AM Rui Barradas <ruipbarradas at sapo.pt> wrote:
Hello, Sorry but after reading my answer I believe it's not completely clear. I meant absolute values, the actual t-scores as computed from the data might be negative. Your code will always produce positive numbers. Hope this helps, Rui Barradas ?s 15:27 de 06/05/20, Rui Barradas escreveu:
Hello, That gives the *absolute* t-scores. If it's all you need/want, then the answer is yes, you can. Hope this helps, Rui Barradas ?s 14:28 de 06/05/20, Ana Marija escreveu:
Hello, Can I apply the quantile function qt() this way? qt(pvals/2, 406-34, lower.tail = F) to get the T-scores? Thanks Ama
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Hello, Another option is to use stats::t.test t.test(x)$statistic Or, if you want to test against a beta0 != 0, t.test(x, mu = beta0)$statistic But in this case the estimator is the estimator for the mean value. Hope this helps, Rui Barradas ?s 15:54 de 06/05/20, Ana Marija escreveu:
Thanks Patrick, so in conclusion this is fine? z-score=Beta/StdErr On Wed, May 6, 2020 at 9:52 AM Patrick (Malone Quantitative) <malone at malonequantitative.com> wrote:
Guessing for Ana, but no, that's a different meaning. Beta/StdErr is a z statistic--a test statistic against (usually) the tails of the unit normal distribution. So like a t-test with infinite df. On Wed, May 6, 2020 at 10:41 AM Rui Barradas <ruipbarradas at sapo.pt> wrote:
Hello,
By z-scores do you mean function help('scale')?
Hope this helps,
Rui Barradas
?s 15:31 de 06/05/20, Ana Marija escreveu:
Hi Rui, Thank you for getting back to me. Is there is a better way to calculate Z scores if I have p values, SE and Beta? Thanks Ana On Wed, May 6, 2020 at 9:27 AM Rui Barradas <ruipbarradas at sapo.pt> wrote:
Hello, That gives the *absolute* t-scores. If it's all you need/want, then the answer is yes, you can. Hope this helps, Rui Barradas ?s 14:28 de 06/05/20, Ana Marija escreveu:
Hello, Can I apply the quantile function qt() this way? qt(pvals/2, 406-34, lower.tail = F) to get the T-scores? Thanks Ama
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
-- Patrick S. Malone, Ph.D., Malone Quantitative NEW Service Models: http://malonequantitative.com He/Him/His
Thank you so much! I mostly worry which of those procedures is the closest to the z-score
On Wed, May 6, 2020 at 10:05 AM Rui Barradas <ruipbarradas at sapo.pt> wrote:
Hello, Another option is to use stats::t.test t.test(x)$statistic Or, if you want to test against a beta0 != 0, t.test(x, mu = beta0)$statistic But in this case the estimator is the estimator for the mean value. Hope this helps, Rui Barradas ?s 15:54 de 06/05/20, Ana Marija escreveu:
Thanks Patrick, so in conclusion this is fine? z-score=Beta/StdErr On Wed, May 6, 2020 at 9:52 AM Patrick (Malone Quantitative) <malone at malonequantitative.com> wrote:
Guessing for Ana, but no, that's a different meaning. Beta/StdErr is a z statistic--a test statistic against (usually) the tails of the unit normal distribution. So like a t-test with infinite df. On Wed, May 6, 2020 at 10:41 AM Rui Barradas <ruipbarradas at sapo.pt> wrote:
Hello,
By z-scores do you mean function help('scale')?
Hope this helps,
Rui Barradas
?s 15:31 de 06/05/20, Ana Marija escreveu:
Hi Rui, Thank you for getting back to me. Is there is a better way to calculate Z scores if I have p values, SE and Beta? Thanks Ana On Wed, May 6, 2020 at 9:27 AM Rui Barradas <ruipbarradas at sapo.pt> wrote:
Hello, That gives the *absolute* t-scores. If it's all you need/want, then the answer is yes, you can. Hope this helps, Rui Barradas ?s 14:28 de 06/05/20, Ana Marija escreveu:
Hello, Can I apply the quantile function qt() this way? qt(pvals/2, 406-34, lower.tail = F) to get the T-scores? Thanks Ama
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
-- Patrick S. Malone, Ph.D., Malone Quantitative NEW Service Models: http://malonequantitative.com He/Him/His