User: liuyang

gravatar for liuyang
liuyang20
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20
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New User
Location:
China
Last seen:
3 years, 8 months ago
Joined:
4 years, 5 months ago
Email:
l******@bmi.ac.cn

Posts by liuyang

<prev • 9 results • page 1 of 1 • next >
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why no replicate samples in ccle mRNA data
... I notice that in ccle(cancer cell line encyclypedia), the mRNA expression data seldom contains replicates for a given cancer cell line. How can I perform differential expression analysis if I want to find differential expressed gene in this cell line? Simply fold change? ...
differential analysis ccle microarray written 3.8 years ago by liuyang20 • updated 3.7 years ago by Biostar ♦♦ 20
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Comment: C: How to get the differentially expressed genes in cancer cell lines
... OK, thanks for your advice! ...
written 3.9 years ago by liuyang20
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Comment: C: How to get the differentially expressed genes in cancer cell lines
... Actually I mean the irregularly up- and down- expressed genes in the cancer cell lines.I need these gene lists for following analysis. So you think it is not suitable to use normal tissue for the comparison?  ...
written 3.9 years ago by liuyang20
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How to get the differentially expressed genes in cancer cell lines
... I'm wondering is there a way to calculate the differentially expressed genes in cancer cell lines(e.g.,MCF7)? The gene expression data (microarray or RNA-seq) for cancer cell lines can be found in many projects, but corresponding normal cell does not exist. Is it sound to use the corresponding norma ...
cancer cell lines differentially expressed genes written 3.9 years ago by liuyang20 • updated 3.9 years ago by Jautis270
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Comment: C: How to compare the gene expression signature of treated cancer cell and normal c
... Sorry for ambiguity, I noticed that I should not compare the profile of normal cell with that of cancer cell line treated with drug directly since this does not make sense. Now I want to collect the differentially expressed genes in the cancer cell lines(PC3, MCF7, etc.). So I need the gene express ...
written 4.4 years ago by liuyang20
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How to compare the gene expression signature of treated cancer cell and normal cell
... I have the gene expression signatures of cancer cell lines and cancer cell lines treated with certain drug. Now I want to analysis if the gene expression of cancer cell treated with the drug is similar with the gene expression of normal cell lines. So I collected the gene expression signatures of no ...
gene expression signature written 4.4 years ago by liuyang20 • updated 4.4 years ago by Jie Ping20
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Comment: C: How to merge zscore value of replicate samples in LINCS data
... Sure now I'm not concerned about the p-value, I just need the combined z-score for subsequent calculations. Finally I take the Stouffer's method. The weight is the average value of spearman coefficient.   ...
written 4.4 years ago by liuyang20
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Comment: C: How to merge zscore value of replicate samples in LINCS data
... Thanks for your suggestion, but the questions is what weight should I give to the different samples. I think arithmetic mean is ok, but how about arithmetic mean weighted by Spearman's rank correlation coefficient?  ...
written 4.4 years ago by liuyang20
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How to merge zscore value of replicate samples in LINCS data
... I'm now working with the LINCS level 4 data. It is the gene expression profiles of human genes when cells are exposed to a variety of perturbing agents. For a single perturbation, there exists many replicate samples. And the LINCS level 4 data provides modified zscore for all the replicates. So if I ...
lincs written 4.5 years ago by liuyang20 • updated 4.5 years ago by Jean-Karim Heriche18k

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Popular Question 4.4 years ago, created a question with more than 1,000 views. For How to compare the gene expression signature of treated cancer cell and normal cell

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