User: b.nota

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b.nota2.2k
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Posts by b.nota

<prev • 324 results • page 1 of 33 • next >
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Comment: C: Error when runing dotplot with enrichGO results
... Hi, I never used this package, but looking at your error only, it seems to indicate that your "ego" object is not a vector. Can you see what "ego" is? head(ego) or str(ego) ...
written 1 day ago by b.nota2.2k
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Answer: A: gogadget: an R package for go analysis visualization and interpretation
... NEWS 2017/01/17 gogadget version 2.0 is now available. It contains a new function called `gogadget.overlap`. This function calculates the overlap index between two GO terms and visualizes it in a heatmap. Furthermore the user's guide is updated, with a detailed explanation of the new function, and ...
written 7 days ago by b.nota2.2k
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Comment: C: How many tests does it take to warrant a microarray/RNA-seq approach to differen
... Did you try something like bioconductor HTqPCR? I never used it myself, but if I had data like yours I would probably try to find something in bioconductor first. ...
written 8 days ago by b.nota2.2k
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Comment: C: Data Analysis with Agilent Microarray RNA Seq Files
... There are also online tutorials available, of course, but the the limma manual is pretty helpful for beginners. It helped me a lot, when I started with it (long ago). ...
written 12 days ago by b.nota2.2k
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Answer: A: Data Analysis with Agilent Microarray RNA Seq Files
... Agilent microarrays are something else than RNAseq. It is both gene expression analysis, but microarrays are not sequencing. Best way to analyze microarrays is with limma in R. There is a very good manual, also describing analysis with Agilent arrays. Good luck! ...
written 12 days ago by b.nota2.2k
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Comment: C: Gene Expression Library
... Where did you look already? I think GEO (https://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (https://www.ebi.ac.uk/arrayexpress/) contains most data sets. ...
written 14 days ago by b.nota2.2k
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Comment: C: How should i start my career in bioinformatics???
... Maybe you should look for a PhD position, e.g. here: https://www.biostars.org/t/Jobs/ And then write a letter? That is usually how I get a job (writing letters). ...
written 19 days ago by b.nota2.2k
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Comment: C: replicates in edgeR and DESeq2
... In your design, your replicates are the group members. So 3 cell lines in "resistant" group and 3 cell lines in "sensitive". If these cell lines should be treated like replicates is a question that you, the scientist, need to answer. Does it make sense to treat these chosen cell lines as members of ...
written 19 days ago by b.nota2.2k
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Comment: C: Summarizing the Results in R
... Yeah or do a de novo assembly first (before blast). Since it's viral it is not that tough for most computers. ...
written 4 weeks ago by b.nota2.2k
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Answer: A: Summarizing the Results in R
... If you import your txt file in R: df <- read.table("file.txt", sep = "\t", header=T) you can simply summarize it with the `table` function: table(df[,2]) ...
written 4 weeks ago by b.nota2.2k

Latest awards to b.nota

Scholar 4 weeks ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Blasting against multiple fasta file
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Bioinformatics freelancers needed
Scholar 7 weeks ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
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Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Blasting against multiple fasta file
Scholar 4 months ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
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