User: Mike

gravatar for Mike
Mike620
Reputation:
620
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Trusted
Location:
UK
Last seen:
4 days, 7 hours ago
Joined:
1 year, 2 months ago
Email:
m***@gmail.com

Posts by Mike

<prev • 161 results • page 1 of 17 • next >
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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 days ago by Mike620
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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 days ago by Mike620
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Comment: C: Seeking private tutor to learn RNA/ChIP-Seq data analysis
... 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 12 days ago by Mike620
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Answer: A: DE analysis using single cell RNA-seq data
... Have a look.. https://www.bioconductor.org/help/workflows/simpleSingleCell/ ...
written 14 days ago by Mike620
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Comment: C: GVSA: problem with gene identifier
... read geneset file in getGmt, Not expression_matrix. genelist_mic <- getGmt(geneset.gmt) ...
written 4 weeks ago by Mike620
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Comment: C: GVSA: problem with gene identifier
... 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 weeks ago by Mike620
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Answer: A: GVSA: problem with gene identifier
... 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 5 weeks ago by Mike620
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Comment: C: extracting the genes associated with the clusters
... 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 11 weeks ago by Mike620
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Comment: C: CCLE expression data file explaination (CCLE_Expression_2012-09-29.res)
... 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 11 weeks ago by Mike620
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CCLE expression data file explaination (CCLE_Expression_2012-09-29.res)
... 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 ...
ccle written 12 weeks ago by Mike620 • updated 11 weeks ago by tszn198490

Latest awards to Mike

Commentator 12 days ago, created a comment with at least 3 up-votes. For C: extracting the genes associated with the clusters
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Single Cell RNAseq data analysis protocol
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: extracting the genes associated with the clusters
Popular Question 3 months ago, created a question with more than 1,000 views. For Single Cell RNAseq data analysis protocol
Student 6 months ago, asked a question with at least 3 up-votes. For How to avoid conversion of gene symbols to date format in Excel
Teacher 7 months ago, created an answer with at least 3 up-votes. For C: Starting a career in Bioinformatics
Student 8 months ago, asked a question with at least 3 up-votes. For How to avoid conversion of gene symbols to date format in Excel
Supporter 8 months ago, voted at least 25 times.
Centurion 8 months ago, created 100 posts.
Teacher 11 months ago, created an answer with at least 3 up-votes. For C: Starting a career in Bioinformatics

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