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Search: Posts Made By: arnoldliao
Forum: Bioinformatics 07-05-2017, 09:20 AM
Replies: 12
Views: 3,926
Posted By arnoldliao
Thank you

Merci for the reply, I got it to work with a correct bed file. I did get many Na . I will email you separately on the issues.
Forum: Bioinformatics 06-14-2017, 09:14 AM
Replies: 12
Views: 3,926
Posted By arnoldliao
mclust error

I figured it out. My be file contain only chr,start,end while ONCOCONV needed chr,start,end,name,score,geneName

I'm getting an error
Error in if (minFrac < minFractionOfShortOrLongAmplicons &...
Forum: Bioinformatics 08-16-2016, 03:08 PM
Replies: 12
Views: 3,926
Posted By arnoldliao
perhaps switching out...

perhaps switching out https://stat.ethz.ch/R-manual/R-devel/library/stats/html/loess.html
for https://stat.ethz.ch/R-manual/R-devel/library/MASS/html/rlm.html ?
Forum: Bioinformatics 08-16-2016, 02:51 PM
Replies: 12
Views: 3,926
Posted By arnoldliao
span is too small

Anyone experience this issue
Error in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, :
span is too small

I assume this is because my bed file contain sections where...
Forum: Bioinformatics 10-07-2010, 10:48 AM
Replies: 23
Views: 10,835
Posted By arnoldliao
IGV scripting function

Use IGV to output plots of a region of a bam file with the following sample script

http://www.broadinstitute.org/igv/batch

attached is an example (note path to bam and snapshotDirectory need to...
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