User: johnsonnathant

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Posts by johnsonnathant

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Comment: C: Combining two rnaseq platforms in one
... I can not thumb up genomax's comment enough ...
written 4 days ago by johnsonnathant70
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Answer: A: Comparing Multiple Species RNA seq data
... Over the year, there have been several papers asking a similar question, but the definite first step in the analysis is determining what is the 'same gene' usually done via orthologues or paralogues. Here are some examples on cross species/genus/organism comparisons: https://www.pnas.org/conten ...
written 5 days ago by johnsonnathant70
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Answer: A: Compare SE and PE gene expression data.
... I also don't think this comparison is a good protocol. If you are trying to ask the question whether there is a difference between SE and PE expression data that would be possible, EXCEPT they are different samples, different labs, and different protocols. How do you know regardless of whatever ...
written 5 days ago by johnsonnathant70
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Comment: C: Comparing stranded reads to unstranded reads
... Ideally, wouldn't mix the datasets, but everything would be done exactly the same. However, there is also the potential for insight if the analysis is done right as it could help highlight whether there is important information gathered from anti-sense transcripts. ...
written 5 days ago by johnsonnathant70
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Comment: C: Combining two rnaseq platforms in one
... It sounds like from the description, you have is Nanostring data, not RNA-Seq? Just to clarify, as RNA-Seq (generally speaking) is probe free. With regards to your comments: "I want to merge these data to have 3000 genes as samples are the same" whenever data is merged, need to always ask whether ...
written 5 days ago by johnsonnathant70
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Comment: C: Humbly Requesting Interviews & Responses on How to Improve Bioinformatics Softwa
... Agreed, this type of question/request is so broad. Each of those topics you listed will have different types of people involved. ...
written 5 days ago by johnsonnathant70
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Comment: C: Comparing stranded reads to unstranded reads
... It depends on how you want to do the analysis. If you are looking for DE genes between both datasets, then it will be difficult to distinguish between genes that are different due to the library prep protocol or the biology of those datasets. If it is possible to mix the two data sets then do the ...
written 5 days ago by johnsonnathant70
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Answer: A: how to interpret NES(normalized enrichment score)?
... I assume the 'NES' type abbreviation is coming from the GSEA analysis that can be commonly run via R (https://bioconductor.org/packages/release/bioc/html/fgsea.html) that was made popular through the BROAD (http://software.broadinstitute.org/gsea/index.jsp). Since its not completely obvious what i ...
written 6 days ago by johnsonnathant70
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Answer: A: Combining two rnaseq platforms in one
... There are several warning flags that come to mind based on the description of the data analysis especially when it comes to developing a predictive model for responder vs non-responder patients. There are many factors such as knowing the specifics on numbers, distribution of data, the similarity of ...
written 6 days ago by johnsonnathant70
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Answer: A: What is RPKM/FPKM > 1 or 3 or 5?
... As mentioned, the purpose is to set a cutoff for what is considered 'expressed'. This is also where the concept of TPM (transcripts per million) started becoming popular rather then RPKM/FPKM since the attempt is to quantify the expression in a complete transcript. For what is considered a good cu ...
written 6 days ago by johnsonnathant70

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Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Combining two rnaseq platforms in one

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