Moderator: Benn
Benn ♦ 7.9k
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Posts by Benn
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... 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 9 weeks ago by
Benn ♦ 7.9k
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... 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 10 weeks ago by
Benn ♦ 7.9k
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... 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 10 weeks ago by
Benn ♦ 7.9k
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... 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 weeks ago by
Benn ♦ 7.9k
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... 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 weeks ago by
Benn ♦ 7.9k
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... 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 weeks ago by
Benn ♦ 7.9k
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... 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 3 months ago by
Benn ♦ 7.9k
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... 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 3 months ago by
Benn ♦ 7.9k
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... To do GO enrichment analysis for more groups in parallel you can try [clusterProfiler][1]. I used it once to do GO enrichment analysis for 6-7 groups simultaneously.
[1]: https://bioconductor.org/packages/release/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html ...
written 3 months ago by
Benn ♦ 7.9k
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Comment:
C: How to normalize my rna seq data?
... You could use [voom][1] normalization from limma, and add the quantile normalization in there with argument `normalize.method = "quantile"`. However, start with real counts, derived from featureCounts instead of RSEM.
[1]: https://www.rdocumentation.org/packages/limma/versions/3.28.14/topics/voo ...
written 4 months ago by
Benn ♦ 7.9k
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