User: Biologist

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Biologist70
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Posts by Biologist

<prev • 102 results • page 1 of 11 • next >
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Comment: C: p-value with chi-square test
... Thank you Kevin. I would also like to know Is it wrong calculation if `correct=TRUE`. At what times it should be TRUE? ...
written 2 days ago by Biologist70
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p-value with chi-square test
... From this Research paper Table1 [Association of RAD51-AS1 expression with clinicopathological features of EOC patients][1] I see that `p-value` is calculated based on Chi-square test. Age Low-RAD51-AS1 High-RAD51-AS1 P-value <50 25 (38.5) 17 (26.6) 0.149 ≥50 40 (61.5) ...
p-value R significant test rna-seq statistics written 2 days ago by Biologist70 • updated 2 days ago by Kevin Blighe25k
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Comment: C: Survival plot between low and high expression of gene
... Thank you. I will do that with normalized counts. And do you think using `rpkm` for the cutpoint a bad idea? ...
written 3 days ago by Biologist70
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Comment: C: Survival plot between low and high expression of gene
... Oh yes. thank you. What could be the reason for that? because of different expression data? And what would you recommend to use for dividing samples into low and high based on expression, normalized counts or rpkm? or fpkm or any other? ...
written 3 days ago by Biologist70
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Survival plot between low and high expression of gene
... Hi, I wanted to make a survival plot showing between low and high expression samples of a gene. I followed this [cutpoint using maxstat package][1] to divide samples into low and high. In that tutorial they used rsem normalised counts gene expression data. I have `raw counts` from featurecounts pa ...
R rna-seq survival geneexpression written 3 days ago by Biologist70 • updated 3 days ago by Santosh Anand3.7k
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Comment: C: Why survival plots look different with same data?
... Yes, I see that in my case I have one sample less. I guess it won't make much difference. In their analysis they removed Genes with FPKM < 1, In my case I'm looking at only single gene. ...
written 11 days ago by Biologist70
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Comment: C: Why survival plots look different with same data?
... Yes, the trend looks same but in my plot I see after 2000 days there is down peak of high expression which I didn't observe in plot in HPA. I have used the same cutoff 23.6 which they have used. Don't know what is that small difference. ...
written 11 days ago by Biologist70
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Why survival plots look different with same data?
... Hello, The survival plot based on `Best separation` of high and low expression samples of `GPAM` with `Expression cutoff` 23.6 FPKM looks like below (This plot is from [Human Protein Atlas database][1]) [Survival Plot between high and low samples of GPAM Expression][2] I took the GPAM FPKM data g ...
survivalanalysis tcga fpkm survival rna-seq written 11 days ago by Biologist70 • updated 11 days ago by Friederike2.0k
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Comment: C: What is the cutoff used for define high or low expression level of gene for surv
... Thank you very much Kevin. ...
written 12 days ago by Biologist70
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Comment: C: What is the cutoff used for define high or low expression level of gene for surv
... Hi Kevin, I would like to look at survival of a specific gene between high and low expression tumor samples. For this, I want to divide tumor samples into high and low. I have counts data and transformed them into z-score. Do you think the below one is right way to divide the samples? event_ ...
written 13 days ago by Biologist70

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Centurion 11 days ago, created 100 posts.
Student 5 weeks ago, asked a question with at least 3 up-votes. For How to make scatterplot with two different results sets?
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