User: yura.grabovska
yura.grabovska • 10
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- Last seen:
- 5 months, 2 weeks ago
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- 2 years, 6 months ago
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Posts by yura.grabovska
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... I am getting this error when trying to biocLite() the latest version:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/****/R/x86_64-pc-linux-gnu-library/3.4/robustbase/libs/robustbase.so':
`maximal number of DLLs reached...
ERROR: lazy loading failed f ...
written 5 months ago by
yura.grabovska • 10
• updated 5 months ago by
Yuan Tian • 40
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... If using the 'minfi' method, you can use 'force = TRUE'. As Yuan said above, the current Illumina EPIC manifest is in its 4th version of revisions. With each version they drop some poor performing probes and I think B3 had some naming issues. The minfi function used by ChAMP will force the import of ...
written 5 months ago by
yura.grabovska • 10
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... Thanks Mike. This makes sense. I'll implement your suggestion.
...
written 14 months ago by
yura.grabovska • 10
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... Edited above to add. Just to add:
Of the original list I fed the function, around 20% weren't matched. I subset those ensembl IDs which were not matched and ran just them (around 5000) through the function again. Most were matched but around 20% weren't matched again. I repeated the process but was ...
written 14 months ago by
yura.grabovska • 10
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... Of the original list I fed the function, around 20% weren't matched. I subset those ensembl IDs which were not matched and ran just them (around 5000) through the function again. Around 20% weren't matched again. I repeated the process but wasn't able to extract the additional missing genes. The fac ...
written 14 months ago by
yura.grabovska • 10
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... I am feeding biomaRt a list of ensembl IDs (object: `ensemblIDs`) from an RNA-Seq experiment
Then I am running the following function calls
ensembl <- useMart('ensembl', dataset='hsapiens_gene_ensembl')
symbols.a <- getBM(attributes = c('ensembl_gene_id',
...
written 14 months ago by
yura.grabovska • 10
• updated 14 months ago by
Mike Smith • 2.9k
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... Thank you for getting back to me. We assumed there was something going on along these lines as I recently had a similar problem with minfi reading in newer EPIC array idats before the update dropped.
Will implement change you recommended.
...
written 14 months ago by
yura.grabovska • 10
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...
Conumee error:
Error in .local(query, ref, anno, ...) :
query intensities not given for all probes.
This error results when I use
x <- CNV.fit(data[1], controls.data, anno)
The data object was generated by:
rgSet <- combineArrays(rgSet.450k, rgSet.850k)
mSet <- preprocessNoob ...
written 14 months ago by
yura.grabovska • 10
• updated 13 months ago by
SplittingInfinity • 30
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... Hi,
I am currently carrying out an analysis on some 450k data to look for sub-grouping. My pipeline has been so far to preprocess the data in minfi and carry out an unsupervised clustering in NMF. With my ranks identified, I took the H values and correlated those to my M-values set. I now have a li ...
written 2.6 years ago by
yura.grabovska • 10
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