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Star20
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Comment: C: combining z-scores into a single z-score value
... Hi. Kevin. Thanks for the reply. At this stage I am trying to find the differential expression of tissues regardless of high expression or decreased expression of genes (if this makes sense). In the sentence you used above, what do you mean by "This will then return 'scores' for the samples in you ...
written 29 days ago by Star20
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Comment: C: Error in "EmpiricalBrownsMethod": Error in data_vector - dvm : non-numeric argum
... Just an update: My input file contained the GeneIds and geneNames as the first two columns (which are not numeric). I deleted these two columns. Rest of the columns in my file were numeric and the command executed. But still I cannot understand what "data_matrix" argument exactly is. :( Any thoughts ...
written 4 weeks ago by Star20
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Comment: C: combining z-scores into a single z-score value
... Thankyou Kevin for the reply. Actually my main goal is to combine either a z-score or p-value so that a single value could be the representative of a single tissue. I was using Stouffer's method initially which did not give the results as expected because Stouffer's method takes into account the dir ...
written 4 weeks ago by Star20
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Error in "EmpiricalBrownsMethod": Error in data_vector - dvm : non-numeric argument to binary operator
... Hi all, I am trying to combine the p-values using the Brown's method available at "https://bioconductor.org/packages/devel/bioc/manuals/EmpiricalBrownsMethod/man/EmpiricalBrownsMethod.pdf" I am trying to run this method using the following command EmpiricalBrownsMethod::empiricalBrownsMethod( ...
R stats brownsmethod p-values written 4 weeks ago by Star20
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Comment: C: combining z-scores into a single z-score value
... I don't know how to interpret the z-scores? I am assuming that I need to convert z-scores into p-values first and CI first? ...
written 4 weeks ago by Star20
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Comment: C: combining z-scores into a single z-score value
... I am trying to find the differentially expressed genes present within the tissues. So I have the z-scores for all the genes in the tissues. I have combined the z-scores for the genes in each tissue and now I want to see if I could identify or rank the tissues based upon their pathogenicity using the ...
written 5 weeks ago by Star20
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Comment: C: combining z-scores into a single z-score value
... Thanks for the clarification kevin Blighe. I have combined the z-scores using Stouffer's method. But am not sure how to interpret it. ...
written 5 weeks ago by Star20
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Comment: C: combining z-scores into a single z-score value
... Thankyou for the clarification zx8754. I confused "sum(p)" with pvalues instead of zscores. Now that I have combined z-scores, I am confused about how to interpret it? Shall I convert the z-scores into p-values(one or two-tailed?) to see the significance? Apologies if the question seems to be naive. ...
written 5 weeks ago by Star20
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Comment: C: combining z-scores into a single z-score value
... what does p stands for here? z-scores? ...
written 5 weeks ago by Star20
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combining z-scores into a single z-score value
... Hi all, I have a list of z-scores (obtained via effect size/std.err of effect size). I want to combine all the z-scores via Stouffer's method but without weights. Till now I have seen "Stouffer.test" implemented in metaseq package but it requires weights along with the z-score. I have tried "sumz" ...
R stats excel bioinformatics statistics written 5 weeks ago by Star20

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