User: lykosherdshep

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Posts by lykosherdshep

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Can ordinal logistic regression be a good method to test correlation?
... Hey, Kevin, I solved it. the colnames in my data are just gene symbol containing non-syntactic character, and R allow non-syntactic column names with backticks surrounding them. so I just add backticks to each gene symbol and it works. I changed the code to below: tcga_clm_logit <- lappl ...
written 5 weeks ago by lykosherdshep70
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Comment: C: Can ordinal logistic regression be a good method to test correlation?
... Thanks for your help, Kevin. ...
written 5 weeks ago by lykosherdshep70
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Comment: C: Can ordinal logistic regression be a good method to test correlation?
... Yes, only the apply function give me a result, I tried the code you gave me again and I can understand the code, but it return a error(Error in eval(predvars, data, env) : object 'NKX3' not found). Maybe there are some conflicts with the package ordinal. I'll try another ordinal logistic regression ...
written 5 weeks ago by lykosherdshep70
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Comment: C: Can ordinal logistic regression be a good method to test correlation?
... Sorry, I also wanted to confirm my uncertain question, I thinks I should stablize the variance to do other analysis with expression values. in my ordinal regression workflow, the gene expression values I use were transformed by vst() function in DESeq2 package. Can this be a acceptable method? an ...
written 5 weeks ago by lykosherdshep70
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Comment: C: Can ordinal logistic regression be a good method to test correlation?
... I have checked tcga_logit_data$gleason_grade and it's a ordered factor. and the number for each group respectively 23, 95, 52, 38, 65 for gleason grade I, II, III, IV, V. the number seems unbalanced. ...
written 5 weeks ago by lykosherdshep70
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Comment: C: Can ordinal logistic regression be a good method to test correlation?
... Thank you, Kevin. Sorry for my unproper description and thanks for your correcting me. I have just tried your code, but it returns me a error- *Error in eval(predvars, data, env) : can't find object 'NKX3'*, It seems the gene symbol name cause such problems. and my code `tcga_clm_logit < ...
written 5 weeks ago by lykosherdshep70
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Can ordinal logistic regression be a good method to test correlation?
... I'm sorry, the description may be too long. I wanted to find gene whose expresison values positively correlate to gleason grade in prostate cancer using TCGA data, the gleason grade is divided into five group according to the gleason scores**(Grade I: gleason scores <= 6; Grade II: gleason sc ...
correlation rna-seq ordinal logistic regression written 5 weeks ago by lykosherdshep70 • updated 5 weeks ago by Kevin Blighe51k
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Comment: A: Add annotation color bar to ggplot objects
... Although this plot has been depicted, I find the plots created by above code have some color which insinuate two different values. It is difficult for us to set complete different color aesthethic in two different plots ,especially for discrete variables. is there any palette for this circumstance? ...
written 10 weeks ago by lykosherdshep70
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Answer: A: Add annotation color bar to ggplot objects
... Thanks for the people helping me in completing this plot. I have created this plot use two different ways, the one uses ggplot2 and cowplot, the other uses ComplexHeatmap here is my code for the data code test <- data.frame(sample = paste0("sample", 1:100), tumor = re ...
written 10 weeks ago by lykosherdshep70
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Comment: C: Add annotation color bar to ggplot objects
... Oh, Thanks, I'll try the package ComplexHeatmap firstly. Thanks for your help ...
written 11 weeks ago by lykosherdshep70

Latest awards to lykosherdshep

Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Add annotation color bar to ggplot objects
Supporter 3 months ago, voted at least 25 times.

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