User: sophiespo

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sophiespo70
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Posts by sophiespo

<prev • 10 results • page 1 of 1 • next >
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Answer: A: gene expression analysis using RNA seq data
... The most popular differential expression algorithms require that you supply raw counts, not FPKM. [DeSeq2][1] [edgeR][2] [Here's a good differential expression workflow using edgeR in R][3] [1]: https://bioconductor.org/packages/release/bioc/html/DESeq2.html [2]: https://bioconductor.org/pa ...
written 8 weeks ago by sophiespo70
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... You have character references in your code, rather than the characters themselves. & amp ; is the character code for & and & nbsp ; is the code for a space (I had to put spaces in). Try: if (x1 != 'NA' & x2 != 'NA'){ lines(c(0,x1),c(0.5,0.5),col='blue') lines(c( ...
written 9 weeks ago by sophiespo70
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Answer: A: Mice driver mutations
... If you're happy to look at CNV as a driving cause of pancreatic cancer, you can use GISTIC2.0 to work on mouse samples and find significant regions of loss and gain. I did this successfully for a mesothelioma mouse model. ...
written 10 weeks ago by sophiespo70
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Answer: A: How to download a full matrix of gene expression HTSEQ counts from all TCGA canc
... You can easily download the counts and create this matrix yourself using the TCGAbiolinks package in R: https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html ...
written 10 weeks ago by sophiespo70
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EnsEMBL Perl API connection error
... Hi all, This is the first time I've had to post for help on something so if I've done it wrong I apologise. I have been writing a script that uses the Bio::EnsEMBL::Registry API. It has been working really well and I've had no issues with it until now. I went away for a week, and upon getting back ...
software error written 6 months ago by sophiespo70 • updated 6 months ago by Astrid_Ensembl170
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Answer: A: How to present mapping result ?
... I can't tell you specifically but I find it is a good exercise to read current sequencing publications and see how they present their mapping stats. I am always looking for nicer ways to present boring numbers like that. ...
written 9 months ago by sophiespo70
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Answer: A: About selection of samples in TCGA
... It might be useful for you to look at the R package TCGA Biolinks (http://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html). It has help information for downloading the clinical information. You could parse the clinical data for the recurrent samples in R, and then you could just downlo ...
written 10 months ago by sophiespo70
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Answer: A: Is DNA or RNA better to get somatic mutation profile for neoantigen estimation?
... Personally, I would design my experiment to use both if I could. I would use DNA sequencing to perform identication of mutations and prediction of neoantigens, then use RNAseq to quantify expression of the neoantigens. Lack of expression of a predicted neoantigen may be just as interesting as findin ...
written 10 months ago by sophiespo70
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Answer: A: Is there any method for using WES data from Illumina Hiseq into ABSOLUTE?
... Hey namhaesly, You need to create segmentation files for your data. You can use VarScan2 (the copynumber) function, or any other program that computes copy number information. My tool of choice is ExomeCNV though I don't know how supported it is these days. Then you can add the mutation informatio ...
written 14 months ago by sophiespo70
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... This is most likely happening due to there being no normal samples in the dataset, so n_index is empty. I don't really know enough about model.matrix to know if this is the correct approach, but by not computing the model.matrix and changing the following line: ex <- voom(x,d,plot=F) to: ...
written 15 months ago by sophiespo70

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