User: zephyr_falcon

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Posts by zephyr_falcon

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Comment: C: NAs in TCGA methylation 450k beta data
... I also asked this to GDC, but they didn't know the details as well. I'm just guessing there were some kind of filtering processes but don't know what exactly they are. Remains a mystery. ...
written 4 weeks ago by zephyr_falcon70
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Comment: C: Somatic mutations per gene
... Yes, I can annotate the mutations using VEP (https://useast.ensembl.org/info/docs/tools/vep/index.html), and then count them per gene on my own. But I just wondered if there's a tool to do all of them automatically. Thanks for your comment anyway. ...
written 4 weeks ago by zephyr_falcon70
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Answer: A: How to interpret the output of gatk?
... It seems like you ran tumor-only mode of Mutect2. Did you only put tumor bam file as an input? Mutect2 needs 2 bam files for accurate mutation calling: tumor and its matching normal. If you just use a tumor bam file, it will also call false positives which may lead to larger number of somatic muta ...
written 4 weeks ago by zephyr_falcon70
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Somatic mutations per gene
... Hi, I have a vcf file (from Mutect2) - list of somatic mutations and their genomic locations & other info. Does anyone know that there is a R package that can calculate the number of somatic mutations per gene? For example, map the somatic mutations in the vcf file to any one gene based on t ...
gene R vcf mutect2 somatic mutation written 4 weeks ago by zephyr_falcon70
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Comment: C: NAs in TCGA methylation 450k beta data
... I already tested the data with detection p-values.. (mentioned in the question) The NAs were produced not because of detection p-values. And it is not a problem of few samples. All samples in TCGA COAD methylation beta values have ~90k NAs - 1/5 of 450K. ...
written 4 weeks ago by zephyr_falcon70
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Answer: A: GEO differential expression analysis
... That's probably because of multiple testing. If you perform DE analysis BEFORE removing duplicates, the number of genes used in DE analysis is larger than that of DE analysis AFTER removing duplicates, and it will end up with lower FDRs because there are more genes. And lower FDR can be leaded to mo ...
written 4 weeks ago by zephyr_falcon70
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Answer: A: AnnotationDbi returns different list of symbols from directly derived list of da
... I found my own answer. It seems like the mogene10sttranscriptcluster.db utilizes org.Hs.eg.db for annotation. And the version of org.Hs.eg.db is different between mogene10sttranscriptcluster.db and AnnotationDbi. I found this because when I loaded different version of org.Hs.eg.db, the same versi ...
written 6 weeks ago by zephyr_falcon70
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NAs in TCGA methylation 450k beta data
... Hi, I have a question about TCGA methylation 450K data. When you look at the TCGA methylation beta values, Level 2 data has all the values, but I found many Level 3 probes have NAs (e.g., cg00000108, cg00000109, etc). Level 2 Composite Element REF Methylated_Intensity Unmethylated_Intensi ...
450k beta tcga methylation na written 6 weeks ago by zephyr_falcon70 • updated 6 weeks ago by Charles Warden7.0k
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AnnotationDbi returns different list of symbols from directly derived list of database itself
... Hi. I'm trying to annotate gene symbols next to probe IDs (Affymetrix Mouse Gene 1.0-ST Array). I used "mogene10sttranscriptcluster.db" package (v8.7.0) of R for the annotation. But here's the problem. 1) Using mogene10sttranscriptcluster.db directly library(mogene10sttranscriptcluster.db) ...
gene R annotationdbi mapids written 8 weeks ago by zephyr_falcon70 • updated 6 weeks ago by zx87547.8k

Latest awards to zephyr_falcon

Student 4 weeks ago, asked a question with at least 3 up-votes. For NAs in TCGA methylation 450k beta data
Scholar 6 weeks ago, created an answer that has been accepted. For A: AnnotationDbi returns different list of symbols from directly derived list of da

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