User: hellocita

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hellocita20
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Posts by hellocita

<prev • 18 results • page 1 of 2 • next >
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Comment: C: should non-protein-coding rna(e.g. lncRNA) be removed in RNA-Seq differential ex
... I see, thank you Michael! ...
written 20 months ago by hellocita20
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Comment: C: should non-protein-coding rna(e.g. lncRNA) be removed in RNA-Seq differential ex
... Hi Michael, I still do not fully understand why the off-target effect are related to the non-coding RNA i got, since the off-target effect are mostly related to siRNA. Do you mean that these genes are called DEGs because off-target effect during the experiment? Therefore one should use different st ...
written 20 months ago by hellocita20
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should non-protein-coding rna(e.g. lncRNA) be removed in RNA-Seq differential expression analysis
... Hi, I was doing RNA-Seq differential expression analysis, I wonder if some non-protein coding genes, such as lnc-rna or the Pseudogene, should be removed before analysis? Since the purpose is to reveal the expression difference of control and observe group, and to relate the difference with some kno ...
rna-seq written 20 months ago by hellocita20 • updated 20 months ago by michael.ante3.6k
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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 2.8 years ago by hellocita20
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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 2.8 years ago by hellocita20 • updated 2.8 years ago by Kevin Blighe68k
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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 2.8 years ago by hellocita20
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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 2.8 years ago by hellocita20
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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 2.8 years ago by hellocita20 • updated 2.8 years 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 3.0 years ago by hellocita20
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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 3.0 years ago by hellocita20 • updated 3.0 years ago by Guangchuang Yu2.4k

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Popular Question 2.7 years ago, created a question with more than 1,000 views. For How to Calculate FDR in permutation F test
Popular Question 2.7 years ago, created a question with more than 1,000 views. For remove batch effect for multiple tumor data

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