User: huynguyen96.dnu

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Posts by huynguyen96.dnu

<prev • 34 results • page 1 of 4 • next >
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How to create a Plink bfile BED from existing FAM and BIM files
... Hello, Initially, I have had a vcf file, then used PLINK to turn it into three plink binary files (i.e., BIM, FAM, and BED). Next, for FAM file, I only preserved samples of my interest using R (from 504 samples, now I just have 503 samples). The same for BIM file, I only kept variant IDs of my i ...
plink written 12 weeks ago by huynguyen96.dnu20
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data values' transformation and P-value of Cox log rank test
... Hi everyone, I have done research on using single and integrative analyses on -omic datasets, including gene expression (EXP), copy number alteration (CNA), and methylation (MET), to classify breast cancer patients. Right now, I coded in R as well as drafted my manuscript already, and sent it out t ...
p-value R cox transformation written 6 months ago by huynguyen96.dnu20
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Kruskal-Wallis test for two groups
... Hi all, I used a clustering tool to partition samples into two groups. Next, I want to see the statistical differences between them in terms of clinical features: Lymph nodes (continuous variables) and tumor stages (categorical variables) Now, I used Kruskal Wallis test for the two clinical feature ...
cluster R kruskalwallis statistics written 8 months ago by huynguyen96.dnu20
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Answer: A: which is better for rna-seq analysis? R or python?
... I think this question is kind of can-not-answer one. It depends greatly on your interest and expertise in either R or Python. ...
written 9 months ago by huynguyen96.dnu20
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Comment: C: Survival Analyisis in cancer patients
... Sorry, it seems that your words are wordy, it is hard to understand what you want to present. Correct me if I am wrong. Briefly, you have a matrix whose rows are patients, columns are genes, elements are expression levels (up or down regulated)? now, you want to related the expression levels of e ...
written 9 months ago by huynguyen96.dnu20
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Comment: C: survival analysis with several conditions
... 1-Assure that you divided the above data frame into two sub data frames: one (I call it as '*df*' in R) whose 'Sample' column only includes group1 (drug_1) versus group3 (WT), the other (I call it as '*df1*' in R) whose 'Sample' column only includes group2 (drug_2) versus group3 (WT) Then, for the f ...
written 9 months ago by huynguyen96.dnu20
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how to compute p-value from Fisher's Z transformation?
... I'm having a list of Pearson's correlation coefficients (r). Then, I performed the Fisher's Z transformation using the formula: z = 1/2 ln(1+r/1-r). Now, I want to compute corresponding p-values for each identified z score. After referring to Google, I detect a formula to compute p-value (two-sided) ...
p-value R statistics written 9 months ago by huynguyen96.dnu20
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Comment: C: survival analysis with several conditions
... 1. To my understanding, drug_1, drug_2 and WT are independent groups/labels. Assure that your wanting to compare overall survival of patients after taking orally drug_1 versus WT, and those after taking orally drug_2 versus WT, so the question is that how many patients are in group 1 (drug_1), group ...
written 9 months ago by huynguyen96.dnu20
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Comment: C: How to reorder the column of the heatmap following the cluster annotation?
... Thanks a a lot. This is the answer I'm looking for. ...
written 9 months ago by huynguyen96.dnu20
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How to reorder the column of the heatmap following the cluster annotation?
... Annotation: > ha = HeatmapAnnotation(IntCl = info2$groups, > CNAcorCl = info$groups, > METcorCl = info1$groups, > col = list(IntCl = c("1" = "turquoise", "2" = "pink"), > CNAcor ...
order complexheatmap heatmap written 9 months ago by huynguyen96.dnu20

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Popular Question 7 weeks ago, created a question with more than 1,000 views. For Missing value where TRUE/FALSE needed in R

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