User: Mike
Mike • 660
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Posts by Mike
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... Thank you very much..
It is working perfectly fine. ...
written 4 weeks ago by
Mike • 660
2
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... Hi all,
I am using R script from Getting Genetics Done ( http://www.gettinggeneticsdone.com/2014/05/r-volcano-plots-to-visualize-rnaseq-microarray.html) to generating Volcano plots but my problem is how to show particular single gene name on volcano plot without any condition (i.e foldchange or p ...
written 4 weeks ago by
Mike • 660
• updated
4 weeks ago by
WouterDeCoster ♦ 20k
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Answer:
A: tcgabioloink level 1 data
... Could you please post your initial code, so it would be easy for others to find out your error. ...
written 3 months ago by
Mike • 660
2
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Answer:
A: survival analysis question
... Hi, please have a look at following post... everything described there in detail..
https://www.biostars.org/p/153013/ ...
written 3 months ago by
Mike • 660
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... I am also big fan of your notes. ChIP-seq and RNA-seq notes are amazing. I would recommend these notes to anyone who learning ChIP-seq and RNA-seq data analysis.
...
written 3 months ago by
Mike • 660
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... Have a look..
https://www.bioconductor.org/help/workflows/simpleSingleCell/
...
written 3 months ago by
Mike • 660
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... read geneset file in getGmt, Not expression_matrix.
genelist_mic <- getGmt(geneset.gmt)
...
written 4 months ago by
Mike • 660
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... Agree with @Lluís R point on the support of Bioconductor.
Anyways, I think there is a problem in reading geneset file. Try with gmt format.
How many geneset are you using ? ...
written 4 months ago by
Mike • 660
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... I also observed same in my cases, so name of gene in gene list (genelist_mic) and your expression matrix should be same. I mean gene "Ysk4" in genelist_mic should be same as "Ysk4" in expression matrix. And one more thing that some TCGA data analysis package automatically convert official gene name, ...
written 4 months ago by
Mike • 660
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... You can use *cutree* function,
cutree(hc, k)
have a look at following links:
http://stackoverflow.com/questions/20912001/extract-groups-from-distance-matrix-using-cutree-in-r
http://stackoverflow.com/questions/11489696/how-to-know-about-group-information-in-cluster-analysis-hierarchical
ho ...
written 5 months ago by
Mike • 660
Latest awards to Mike
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For Single Cell RNAseq data analysis protocol
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For C: extracting the genes associated with the clusters
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For A: Single Cell RNAseq data analysis protocol
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5 months ago,
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For C: extracting the genes associated with the clusters
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For Single Cell RNAseq data analysis protocol
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9 months ago,
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For How to avoid conversion of gene symbols to date format in Excel
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For C: Starting a career in Bioinformatics
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11 months ago,
asked a question with at least 3 up-votes.
For How to avoid conversion of gene symbols to date format in Excel
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11 months ago,
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Teacher
14 months ago,
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For C: Starting a career in Bioinformatics
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