User: user31888

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user3188830
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9 hours ago
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3 years, 2 months ago
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Posts by user31888

<prev • 60 results • page 1 of 6 • next >
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Comment: C: What batch correction was applied to pan-Cancer mRNA expression data?
... @i.sudbery: That's right. ...
written 2 days ago by user3188830
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Comment: C: What batch correction was applied to pan-Cancer mRNA expression data?
... Thanks @i.sudbery ! You are right, the expression data from the different TCGA cancer types have been obtained from Firehose pipelines and merged together to form the pan-Cancer Atlas expression matrix 'EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv'. Looking at the pipelines used on Fi ...
written 2 days ago by user3188830
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What batch correction was applied to pan-Cancer mRNA expression data?
... I would need to retrieve the normalisation (and maybe the batch correction method) used to produced the pan-Cancer Atlas mRNA expression matrix (file called 'EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv' found [here][1]). Starting from the raw read counts obtained from the GDC and the ...
mrna pan-cancer atlas tcga normalisation written 5 days ago by user3188830 • updated 5 days ago by i.sudbery3.1k
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Comment: C: How to normalize median-center log-transform an expression matrix
... Ok, I see. The median centering is done by columns (samples), right? ...
written 28 days ago by user3188830
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How to normalize median-center log-transform an expression matrix
... Hi, I often read in articles that read count RNASeq expression matrices (rows=genes / columns=samples) have been fpkm-normalized, median-centered, log2 transformed. In which order these steps are performed? When you do median-centering, you substract from the expression value the median calculate ...
R rna-seq written 28 days ago by user3188830
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Comment: C: Retrieve TCGA file ID and associated barcode with TCGAbiolinks: "GDC server down
... My mistake. I just had to get rid of the `datatable` from the `DT` package (cannot open browser on the server I use anyway). ...
written 5 months ago by user3188830
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Comment: C: Retrieve TCGA file ID and associated barcode with TCGAbiolinks: "GDC server down
... Works ! However, it cannot find function `datatable` in the second part of the code. > datatable(getResults(query, rows = 1:100,cols = c("file_name","cases")), filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), ...
written 5 months ago by user3188830
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Comment: C: Convert GDCResults object (nested lists) to a human readable data frame
... Correct. `as.data.frame.GDCResults` appears in the v1.2.0 and 1.5.4 helpers. But still: > test = cases() %>% filter(~ project.project_id=='TCGA-CHOL') %>% results(n=10) %>% as.data.frame.GDCResults() Error in as.data.frame.GDCResults(.) : could not find function "as.data.f ...
written 6 months ago by user3188830
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Comment: C: Convert GDCResults object (nested lists) to a human readable data frame
... Installed `GenomicDataCommons v1.5.4` on macOS WITHOUT updating dependencies. I can connect to the GDC server. But the function `as.data.frame` still not working (note that `as.data.frame.GDCResults` does not seem to exist). > source('https://bioconductor.org/biocLite.R') > biocLite(' ...
written 6 months ago by user3188830
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Comment: C: Convert GDCResults object (nested lists) to a human readable data frame
... I've just reinstalled GenomicDataCommons and all the dependencies. I cannot connect to the server anymore neither. > source('https://bioconductor.org/biocLite.R') > biocLite('Bioconductor/GenomicDataCommons') > library(GenomicDataCommons) > test = cases() %>% filter ...
written 6 months ago by user3188830

Latest awards to user31888

Popular Question 6 days ago, created a question with more than 1,000 views. For bam-readcount installation problem: Linking CXX executable
Popular Question 13 days ago, created a question with more than 1,000 views. For bam-readcount installation problem: Linking CXX executable
Popular Question 5 months ago, created a question with more than 1,000 views. For bam-readcount installation problem: Linking CXX executable
Popular Question 5 months ago, created a question with more than 1,000 views. For GATK DepthOfCoverage: 'total coverage' and 'mean coverage' meaning
Popular Question 7 months ago, created a question with more than 1,000 views. For bam-readcount installation problem: Linking CXX executable
Popular Question 7 months ago, created a question with more than 1,000 views. For GATK DepthOfCoverage: 'total coverage' and 'mean coverage' meaning
Popular Question 15 months ago, created a question with more than 1,000 views. For bam-readcount installation problem: Linking CXX executable
Popular Question 15 months ago, created a question with more than 1,000 views. For GATK DepthOfCoverage: 'total coverage' and 'mean coverage' meaning
Popular Question 15 months ago, created a question with more than 1,000 views. For GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
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Popular Question 21 months ago, created a question with more than 1,000 views. For GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error

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