User: Mike
Mike • 620
- Reputation:
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Posts by Mike
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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 4 weeks ago by
Mike • 620
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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 5 weeks ago by
Mike • 620
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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 6 weeks ago by
Mike • 620
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... Have a look..
https://www.bioconductor.org/help/workflows/simpleSingleCell/
...
written 6 weeks ago by
Mike • 620
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... read geneset file in getGmt, Not expression_matrix.
genelist_mic <- getGmt(geneset.gmt)
...
written 9 weeks ago by
Mike • 620
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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 9 weeks ago by
Mike • 620
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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 9 weeks ago by
Mike • 620
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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 3 months ago by
Mike • 620
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... Thank you very much @tszn1984, so what do you mean by detection ? undetected mean not expressed? Am I right ? but in above example cell line (7860_KIDNEY, gene/probe= PTPN21/1320_at, expression value = 4.289519, and detection = A). how to proceed this data ? should I exclude all undetected samples ...
written 3 months ago by
Mike • 620
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... Hi all,
I have CCLE expression data file "CCLE_Expression_2012-09-29.res" downloaded from CCLE Broad (broadinstitute.org). Could you please help me what are "A", "P" and "M" columns in data matrix file.
*example data file (CCLE_Expression_2012-09-29.res)*
Description Accession LN18 ...
Latest awards to Mike
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6 weeks ago,
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For C: extracting the genes associated with the clusters
Appreciated
3 months ago,
created a post with more than 5 votes.
For A: Single Cell RNAseq data analysis protocol
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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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For How to avoid conversion of gene symbols to date format in Excel
Teacher
8 months ago,
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For C: Starting a career in Bioinformatics
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9 months ago,
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For How to avoid conversion of gene symbols to date format in Excel
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12 months ago,
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For C: Starting a career in Bioinformatics
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