User: jaro.slamecka

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Mitchell Cancer Institute, University of South Alabama
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Posts by jaro.slamecka

<prev • 7 results • page 1 of 1 • next >
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Answer: A: transfer from computations to experiments?
... If you have a hankering for the wet-lab side of biological research, definitely go for it, I'm sure you can find a good lab for which your computational skills will be an asset. An ideal lab for you will have the following: 1. it will have a track record of good research behind it and several diver ...
written 7 months ago by jaro.slamecka40
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Comment: C: Removing batch effect
... The batch effect would indeed be a major problem. You can remove batch effects when you have sample replicates spread across the different batches (and account for it in the model matrix in limma) but if that's not the case, it may be difficult or impossible since the batch effects could completely ...
written 8 months ago by jaro.slamecka40
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Comment: C: Rna-Seq Biological Replicates...
... I'm guessing the reviewer feels like the experiment may not have been powerful enough. Assuming the two replicates within the control and experimental groups cluster together and there is a reasonable difference between the groups, what you could consider is making a list of interesting targets from ...
written 8 months ago by jaro.slamecka40
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Comment: C: Tools for finding tissue specific gene expression "markers"?
... A great tool for this would be CellNet from Patrick Cahan's lab, it can classify your samples into a variety of tissues based on gene regulatory networks. But it's only available for human and mouse data so far. However, it includes tools for it to be trained for other species. I understand it may n ...
written 10 months ago by jaro.slamecka40
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Comment: C: Heatmap for differential gene expressions
... Your `etp` object only contains ranked genes based on the evidence of differential expression. So you can't use it because it no longer has the actual expression values. But you need it to first decide which genes you want to plot onto the heatmap by taking them out of `etp` first by doing something ...
written 10 months ago by jaro.slamecka40
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Answer: A: Heatmap for differential gene expressions
... Hi Sharon, you're calling the heatmap.2 function on a vector of fold changes (etp$table$logFC). You should call it on a matrix of normalized expression values in dge$E. Before that, subset the dge object based on the most interesting top tags from etp. ...
written 10 months ago by jaro.slamecka40
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Answer: A: extract only geneID and gene symbol from GTF file
... For those who want to use R directly, there is indeed a fast and efficient way to do it, using package "refGenome", first create and empty refGenome object, then read the GTF file in and finally subset the data.frame to only keep gene IDs and symbols library(refGenome) gtf = ensemblGenome() ...
written 13 months ago by jaro.slamecka40

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