User: hwu12

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hwu1250
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Posts by hwu12

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Homologs between tomato and Arabidopsis
... Thanks :-) It is just a little sad that the homologs are based on TAIR10 and an older version of Tomato transcriptome. I guess If I want to use the latest version of tomato annotation and Araport 11 annotation, I will have to blast them myself. ...
written 10 days ago by hwu1250
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Comment: C: Homologs between tomato and Arabidopsis
... It seems to me that the orthoDB is for checking few genes. Can we use it to generate a list of all homolog pairs between two species? Thanks! ...
written 11 days ago by hwu1250
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Homologs between tomato and Arabidopsis
... I was wondering if there is a database for the homologs between two plants. Specifically, I am looking for a list of homologs between tomato and Arabidopsis. Thanks! ...
genome homology written 11 days ago by hwu1250 • updated 11 days ago by h.mon7.5k
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Comment: C: Differential expression for two very different samples
... Thanks so much, James! For others interested in this method, a user's guide can be found at https://github.com/stephaniehicks/qsmooth/blob/master/vignettes/qsmooth-vignette.pdf ...
written 11 days ago by hwu1250
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Comment: C: Differential expression for two very different samples
... It is a very good idea to prioritizing genes instead of normalizing genes. Thanks, Michele. ...
written 11 days ago by hwu1250
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Comment: C: How to compare two very different NGS samples?
... I know people use a selected set of housekeeping genes as controls for qPCR analysis. Could we do that in RNA-Seq analysis? Could you provide a reference for that? Thanks! ...
written 14 days ago by hwu1250
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Comment: C: How to compare two very different NGS samples?
... Thanks, h.mon! This link you suggested does provide a nice example. ...
written 14 days ago by hwu1250
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Comment: C: How to compare two very different NGS samples?
... Please correct me if I am wrong. I guess it is difficult to get "normalized counts" for very different samples. Indeed, most people just go head use these tools with different organs or tissues, but I just wonder if there is a better way. :-) Another way to think about this, maybe it is meaningless ...
written 14 days ago by hwu1250
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Comment: C: How to compare two very different NGS samples?
... e.g. For example: "Still, it is important to keep in mind that even these methods are based on an assumption that most genes are equivalently expressed in the samples." from https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-91 ...
written 14 days ago by hwu1250
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Differential expression for two very different samples
... Standard tools for differential expression analysis tools (e.g. edgeR and DESeq2) assume that most genes in the samples are equally expressed, and only a small fraction of genes are differentially expressed. I was wondering how we can compare two very different RNA samples. For example, one from mus ...
rna-seq statistics written 14 days ago by hwu1250 • updated 12 days ago by James Ashmore1.7k

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