Moderator: Benn

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Benn8.0k
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Posts by Benn

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Comment: C: gogadget: an R package for go analysis visualization and interpretation
... Hi Jenny, You are right, the heatmap and overlap function are to pair wise compare the GO terms from the same experiment. The idea behind it is that many GO terms are actually very similar (share the same genes) but are called slightly different. These heatmaps are meant to group the redundant GO t ...
written 10 weeks ago by Benn8.0k
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Comment: C: gogadget: an R package for go analysis visualization and interpretation
... Hi Jenny, I have not tried to use a different enrichment method, but depending on what function you want to use, I think it is possible. You'll need to rename your columns probably, so that the function will recognize what column to use. If you type in the function in your console you can see how ...
written 10 weeks ago by Benn8.0k
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Comment: C: Deferentially Expressed Genes Heatmap
... Your question is very general, my advice is to find some tutorials on Google and try them first. Then if you run into some problems, come back here with a more specific question and share your code thus far. Good luck. ...
written 11 months ago by Benn8.0k
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Comment: C: Hi, I have 19 RNAseq data(9 control,10 cancer) with CSV format and i want to per
... Try to read the DEseq manual first please, if you run into something specific doing that you can ask here for help. Your question now is too general. ...
written 11 months ago by Benn8.0k
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Answer: A: Calculating Pairwise Alignment Scores
... Gap opening penalty, is the number of points you'll have to subtract when a gap starts (12 in your case with blosum62), and extension penalty is when the gap extents further after opening (so each additional gap after the first opening one). When a gap closes and a new gap opens, you'll get a new o ...
written 11 months ago by Benn8.0k
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Comment: C: cant find output after featureCounts
... I have never used the program in R, but I think your reads counts table will be saved in R object `newcount`. Can you check that object with e.g. head? head(newcount) ...
written 11 months ago by Benn8.0k
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Answer: C: Potential post-doc PI giving exam as part of hiring process
... I think you are right, this is not normal. I think the PI is somewhat overzealous and too enthusiastic, and doesn't realize the time and effort you'll have to spend in this little exam. I think you made the right decision with rejecting the offer. When I had job interviews, sometimes I got the "exam ...
written 11 months ago by Benn8.0k
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Answer: A: Deferentially Expressed Genes using Genes count data obtained from RNASeq
... A good way to start is reading the manual of [limma][1]. Read about the RNA-seq methods and follow some of the case studies. Good luck. [1]: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf ...
written 12 months ago by Benn8.0k
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Comment: C: Enriched GO terms not present in background annotation: BLAST2GO
... How did you do enrichment, with which package? It might be that your BLAST2GO annotation is older than the GO database that was used for enrichment analysis. The GO database is very dynamic and changes with every update. So please explain more about how you did the enrichment analysis. ...
written 12 months ago by Benn8.0k
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Answer: A: Single-color and two color Agilent array analyzing in R
... Two-channel (color) microarrays are usually normalized with LOESS, but one-channel arrays usually only with a between-array method (like quantile). The best tool to use is [limma][1], you can read in the manual how to normalize and analyze these different array types, including case studies with scr ...
written 12 months ago by Benn8.0k

Latest awards to Benn

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: trimming the paired end reads with cutadapt
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Popular Question 6 months ago, created a question with more than 1,000 views. For phred 33 from Ion S5?
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Popular Question 9 months ago, created a question with more than 1,000 views. For phred 33 from Ion S5?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: trimming the paired end reads with cutadapt
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Scholar 14 months ago, created an answer that has been accepted. For C: Find genes of enriched known motif results in HOMER
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Commentator 17 months ago, created a comment with at least 3 up-votes. For C: RNA to protein in bash?
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