User: Mdeng

gravatar for Mdeng
Mdeng510
Reputation:
510
Status:
Trusted
Location:
Germany
Last seen:
4 days, 21 hours ago
Joined:
8 years, 2 months ago
Email:
m********@googlemail.com

Foo is not one bar.

Posts by Mdeng

<prev • 56 results • page 1 of 6 • next >
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Answer: A: Problems with FirebrowseR - query limit sizes
... The problem is this exception In addition: Warning message: In download.Data(url, format, page) : The API responded with code 414. Your query might be to big In this case, the API does not return any data. Hence, `mRNA.Exp` remains empty and accessing it with `mRNA.Exp[[page.Counter ...
written 4 days ago by Mdeng510
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Comment: C: Reference and dbSNP incompatibility issue (MuTect2)
... This is pretty useful. THX ...
written 2.9 years ago by Mdeng510
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Answer: A: FirebrowseR retrive all the genes expression
... Sadly the API is not designed for these purposes. It's likely more intended to provide a light interface for pre-build queries, which e.g. could be included in an application etc.. To bulk download data sets for an entire cohort I would recommend using [GDAC][1] or you could still user FirebrowseR ...
written 3.2 years ago by Mdeng510
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Answer: A: Point mutation as parameter in firebrowseR
... This is something that is not covered within the Firebrowse API and since FirebrowseR is just an API client, it's not within there as well. When you have your data.frame of your desired mRNA / APC samples at hand, just use the their "tcga_participant_barcode" column and run the "Analyses.Mutation.MA ...
written 3.6 years ago by Mdeng510
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Comment: C: data matrix from firebrowser figure
... The viewGene expression visualizer just uses the mRNA data available thru the Firehose API (see here). The RSEM Score they use for plotting is already included when retrieving data from the API. This is also said when you klick the "help" on your link. ...
written 3.6 years ago by Mdeng510
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Comment: C: TCGAs CNV (SNP Array) level 3 data, confusing descriptions
... Exactly. And for those which are controlled with a normal sample, the analysis pipeline is not clear to me. Let's say for one patient the region chr1:1000-1200 has a seqMean of 0.2 in the normal and 0.7 in the tumor sample. What do I get when download the T and N sample? Reading SNP array-based dat ...
written 5.1 years ago by Mdeng510
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TCGAs CNV (SNP Array) level 3 data, confusing descriptions
... Hello everyone, again I am struggling with getting TCGAs data and description together. As the title says, it's about CNV data by SNP Arrays. Reading the wiki page SNP array-based data it says, Level 3 data describes regions of the genome that seem to have segmental duplications or deletions in t ...
unpaired paired tcga cnv level3 written 5.1 years ago by Mdeng510 • updated 4.9 years ago by roelverhaak0
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Comment: C: Tcga: "Tumor, Matched Normal" Vs. "Normal, Matched Tumor"
... Yes, thank you. This should be written down somewhere within TCGAs wiki. ...
written 5.1 years ago by Mdeng510
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Comment: C: TCGAs Methylation Data Annotation
... Perfect, this is what I was looking for. Thanks you very much! ...
written 5.4 years ago by Mdeng510
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TCGAs Methylation Data Annotation
... Hello everyone, I got a question regarding TCGAs Methylation data. I downloaded it via the "Data Matrix", 98 Samples, 49 pairs of Tumor/Normal tissue, all Level 3 and all from Illuminas HumanMethylation450 Chip. Everything is prostate cancer. So, looking at the data, there ~25% of the symbols missi ...
annotation tcga methylation written 5.4 years ago by Mdeng510 • updated 5.4 years ago by Charles Warden7.2k

Latest awards to Mdeng

Appreciated 2.9 years ago, created a post with more than 5 votes. For A: How To Make A Circular Plot Of Snps And Indels ??
Great Question 2.9 years ago, created a question with more than 5,000 views. For Varscan, Using The Copycaller
Great Question 2.9 years ago, created a question with more than 5,000 views. For Work With Dnacopy (Bioconductor) And Varscan Copynumber Results
Popular Question 2.9 years ago, created a question with more than 1,000 views. For TCGAs CNV (SNP Array) level 3 data, confusing descriptions
Epic Question 3.2 years ago, created a question with more than 10,000 views. For Tcga: "Tumor, Matched Normal" Vs. "Normal, Matched Tumor"
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Grouping Cnv After Segmentation Using Bioconductor Dnacopy
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Go Terms From Ensembl
Commentator 3.4 years ago, created a comment with at least 3 up-votes. For C: Tcga: "Tumor, Matched Normal" Vs. "Normal, Matched Tumor"
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Link Between Ensembl And Omim
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: How To Make A Circular Plot Of Snps And Indels ??
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Work With Dnacopy (Bioconductor) And Varscan Copynumber Results
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Link Between Ensembl And Omim
Great Question 4.4 years ago, created a question with more than 5,000 views. For Tcga: "Tumor, Matched Normal" Vs. "Normal, Matched Tumor"
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Your Favorite Mapper For What Kind Of Data?
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Link Between Ensembl And Omim
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Your Favorite Mapper For What Kind Of Data?
Student 4.8 years ago, asked a question with at least 3 up-votes. For Your Favorite Mapper For What Kind Of Data?
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Tcga: "Tumor, Matched Normal" Vs. "Normal, Matched Tumor"
Appreciated 5.5 years ago, created a post with more than 5 votes. For A: How To Make A Circular Plot Of Snps And Indels ??
Good Answer 5.5 years ago, created an answer that was upvoted at least 5 times. For A: How To Make A Circular Plot Of Snps And Indels ??
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Using Gatk, Removing Read Contigs On Bam Level
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Varscan, Using The Copycaller
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Work With Dnacopy (Bioconductor) And Varscan Copynumber Results
Supporter 5.5 years ago, voted at least 25 times.
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Performance Bottlenecks In Next Generation Sequence Analysis Pipeline

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