User: Mattias Aine

gravatar for Mattias Aine
Mattias Aine570
Reputation:
570
Status:
Trusted
Location:
Sweden
Twitter:
@MattiasAine
Scholar ID:
Google Scholar Page
Last seen:
1 year, 10 months ago
Joined:
5 years, 4 months ago
Email:
m***********@gmail.com

about me

Posts by Mattias Aine

<prev • 21 results • page 1 of 3 • next >
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Answer: A: Silhouette plots in R
... So you want to cluster the columns or the rows, I interpret your question as pertaining to columns!? Your code currently calculates the distance for rows. dis <- vegdist( t(exp_mat) ) #distance for samples/columns Also you mention correlation but vegdist by default calculates Bray-distanc ...
written 2.4 years ago by Mattias Aine570
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Comment: C: Meaning of TCGA CNV data
... Because every sample has one run on normal (usually) blood DNA as well as one tumor tissue. This gets us to 2 files per sample. Running a blood normal as well as tumor sample allows you to filter out private natural copynumber changes from the patient data so you know what is really a tumor related ...
written 2.4 years ago by Mattias Aine570
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Comment: C: Integrating DMR data
... Are we done then or is there anything else? ...
written 2.4 years ago by Mattias Aine570
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Comment: C: Integrating DMR data
... Strange, works fine for me.. How bout this then? d<-do.call("cbind",lapply(elementMetadata(myRanges),as.vector)) ...
written 2.4 years ago by Mattias Aine570
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Comment: C: Integrating DMR data
... ok, think it should work but then which one of these fails? a<-as.vector(seqnames(myRanges)) b<-start(myRanges) c<-end(myRanges) d<-as(elementMetadata(myRanges),"matrix") If none then check that they are all same length or dimensions length(a) dim(d) ...
written 2.4 years ago by Mattias Aine570
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Answer: A: Meaning of TCGA CNV data
... Sample should be the unique sample identifier for this SNP-array experiment, it corresponds to a unique sample run by TCGA and can be a normal or tumor sample. Will map to a unique id like this: https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode The rows correspond to contiguous chunks along the c ...
written 2.4 years ago by Mattias Aine570
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Comment: C: DNA differential methylation analysis for Illumina Human Methylation 450k and 27
... Possibly, the platform is fairly robust but always do a sanity check on the results. A potential problem could of course be if 'group1' has been run on 27K and 'group2' on 450. Then you cant really say the results are due to a true g1-g2 difference. Although I could still believe the results if you ...
written 2.4 years ago by Mattias Aine570
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Comment: C: Integrating DMR data
... If you just write the name of the results object 'myRanges' what does that look like? myRanges #type this in R and press enter Anything to write to file there? ...
written 2.4 years ago by Mattias Aine570
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Comment: C: Integrating DMR data
... Please add the full code chunk with error messages. ...
written 2.4 years ago by Mattias Aine570
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Answer: A: Integrating DMR data
... Assuming you have the coordinates for DMRs in each of the samples and can get them into R it's fairly simple using GenomicRanges. Here is a simple example of how you could try to get it done starting with e.g. BED-like coordinates for your peaks. Might have some bugs but if you're lucky it works st ...
written 2.4 years ago by Mattias Aine570

Latest awards to Mattias Aine

Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Example publications for Individualized Medicine
Scholar 2.4 years ago, created an answer that has been accepted. For A: Example publications for Individualized Medicine
Scholar 2.4 years ago, created an answer that has been accepted. For A: Example publications for Individualized Medicine
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Example publications for Individualized Medicine
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Gene Expression Pam Classification Reproducibility Question
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
Scholar 4.9 years ago, created an answer that has been accepted. For A: Example publications for Individualized Medicine
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Example publications for Individualized Medicine
Scholar 5.2 years ago, created an answer that has been accepted. For A: Example publications for Individualized Medicine
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Example publications for Individualized Medicine

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