User: kevin.m.hao

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kevin.m.hao10
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Posts by kevin.m.hao

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Comment: C: avereps(): 'ProbeName' or 'SystematicName' for agilent one-channel microarray?
... Hi Gordon, If one does not average replicate probes, then limma does identify the Differentially Expressed Probes (DEP), right? After obtaining DEP, how to transform to Differentially Expressed Genes (DEG) from these DEPs? Thanks. ...
written 2.6 years ago by kevin.m.hao10
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Comment: C: avereps(): 'ProbeName' or 'SystematicName' for agilent one-channel microarray?
... Or can one first use "ProbeName" to averge the duplicated probes and then use "SystematicName" to focus one the genes/transcripts? That is a two-step procedure. Is it reasonable to do this? ...
written 2.6 years ago by kevin.m.hao10
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Comment: C: avereps(): 'ProbeName' or 'SystematicName' for agilent one-channel microarray?
... Thanks James. But what case should one take the average of all duplicate probes? If I understand right, in most situations, one would like to get the differentially expressed genes (DEG) no the probes, right? Even one get the DE probes, they should map these probes to genes, so it is more direct to ...
written 2.6 years ago by kevin.m.hao10
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avereps(): 'ProbeName' or 'SystematicName' for agilent one-channel microarray?
... Hello, I am using Limma to analyze one-channel agilent microarray data from NCBI GEO (GSE57296) from raw data. In the step of avereps(), I notice that one can  yave <- avereps(y0, ID = y0$genes[, "SystematicName"]) # "SystematicName" OR yave <- avereps(y0, ID = y0$genes[, "ProbeName"]) # ...
microarray limma written 2.6 years ago by kevin.m.hao10 • updated 2.6 years ago by Gordon Smyth38k
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Comment: C: Confusing: identify differentially expression genes (DEG) perturbed by a drug in
... Thanks Aaron. By comparison of the DEG lists by computing the gene list similarity using for example 'biological process, BP', one may identify if the two perturbations have the same action to certain diseases. If so, drug repositioning may be generated, right? I am still confusing that how to ex ...
written 2.7 years ago by kevin.m.hao10
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Comment: C: Confusing: identify differentially expression genes (DEG) perturbed by a drug in
... Thanks Aaron. If I just know drugA and rnaA were both tested in the same cell lines such as MCF7 (homo), but I do not know if other experimental factors (such as concentrations, time etc) are same (due to that they are from different researchers' experiment), can I compare the DEG lists perturbed b ...
written 2.7 years ago by kevin.m.hao10
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Comment: C: Confusing: identify differentially expression genes (DEG) perturbed by a drug in
... Thanks Gordon. I modified the typos I made before. Now it is 16 microarrays. In fact, my goad is that: I would like to compare DEGs induced by two kinds of perturbations (e.g., one is drugA, and another is rnaA). However, I can not do wet experiment for that, so I just want to analyze the exisiting ...
written 2.7 years ago by kevin.m.hao10
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Confusing: identify differentially expression genes (DEG) perturbed by a drug in Limma
... Hello, I would like to identify the Differentially Expressed Genes (DEG) perturbed by a drug 'metformin'. The experiment is one-color microarray as shown below. The 'controlFileName' refers to the array without the drug (metformin here) treatment, and 'perturbationFileName' refers to the correspon ...
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Comment: C: One replicate (one-color OR two-color) is enough to use Limma?
... Thanks Gordon. Will follow your suggestions. ...
written 2.7 years ago by kevin.m.hao10
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Comment: C: One replicate (one-color OR two-color) is enough to use Limma?
... Thanks Gordon. I modified the statements "...Limma refuses analysis in the step" according to you. Yes. I am trying to learning other people's work. They did analysis like this: If microarray is two-color: they identified DEG just using 2-fold change, no matter if there exists replicates. If microar ...
written 2.7 years ago by kevin.m.hao10

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