User: hellocita

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hellocita10
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Posts by hellocita

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Comment: C: will different proportion of control/patient samples affect gene's Pearson corre
... Thank you Kevin! However i am not sure whether I can use WGCNA, because it may be first calculate gene module by correlation based on control sample, so I think it may not reflect what really happened in disease sample, disease sample module should be different from control module I think. ...
written 15 days ago by hellocita10
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will different proportion of control/patient samples affect gene's Pearson correlation?
... I have rna-seq data that were from different ages(10, 20, 30, 40, 50 year-old) in 50 control and 14 patients. And based on differential analysis I found some differential genes across age. I want to divide genes into several cluster by using their pearson correlation r for hierarchical clustering, a ...
pearson correlation hierarchical clustering written 21 days ago by hellocita10 • updated 19 days ago by Kevin Blighe13k
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Comment: C: Why does GO enrichment result give different results when gene list cutoff chang
... thank you @theobroma22, but how can I trust the enrichment result if they will be changed when FDR of gene list is changed? ...
written 22 days ago by hellocita10
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Comment: C: Why does GO enrichment result give different results when gene list cutoff chang
... Thank you @Martombo, the gene number change should be the reason. On FDR 10%, I have 390 genes in list and 20 GO terms enriched(BH corrected fisher test p-value <0.05). However on FDR 5% , I have only 76 genes in list and no GO terms called significant, even if I relax the p-value to be higher(fi ...
written 22 days ago by hellocita10
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Why does GO enrichment result give different results when gene list cutoff change?
... I am new to GO annotation. I use DAVID to do GO annotation, which calculate the gene overrepresentation by fisher exact test. I have gene list with FDR cutoff, in my point of view, if I choosing FDR <= 10% gene for GO annotation, the matched GO terms should have some overlap with FDR <= 5% one ...
gene rna-seq written 23 days ago by hellocita10 • updated 23 days ago by theobroma221.1k
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Comment: C: PANTHER and DAVID can't recognized some Ensembl gene ID?
... Thank you Guangchuang! This package is very useful! The only problem is I need to updated my R version:) ...
written 11 weeks ago by hellocita10
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PANTHER and DAVID can't recognized some Ensembl gene ID?
... Hi all, I am trying to do GO terms annotation using a set of interesting human genes(with Ensembl gene id) and background, they are from RNA-seq data. However, whether I using PANTHER or DAVID, there's always more than 20% gene ids can't be mapped and I want to save these unmapped ids. I have try us ...
gene rna-seq written 11 weeks ago by hellocita10 • updated 11 weeks ago by Guangchuang Yu1.7k
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batch effect of repeated experiment
... I have a transcriptomic dataset that has three batches, when PCA analysis, there is intra batch effect in batch 1. Therefore we repeated the experiment in three new batches, using the same samples but random their orders so they randomly allocated to the new batches. The result of the repeated exper ...
gene R rna-seq written 4 months ago by hellocita10 • updated 3 months ago by Biostar ♦♦ 20
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Answer: A: Gwas - Permutation Testing?
... hi Darren, a paper might help you:[enter link description here][1], it explains how FDR in permutation calculate:) [1]: https://academic.oup.com/bioinformatics/article/21/23/4280/194680/A-note-on-using-permutation-based-false-discovery ...
written 10 months ago by hellocita10
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How to Calculate FDR in permutation F test
... Hi all, I am a little confused about how to calculate FDR after permutation F test. Assume there is 6000 genes in my data. And for each gene, I perform 1000 permutation F test and got 1000 F value, which includes 1 original F value and 999 permutating F value. And p-value = sum(F > F-original) ...
R written 10 months ago by hellocita10 • updated 10 months ago by Jean-Karim Heriche14k

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