User: yura.grabovska

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Posts by yura.grabovska

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ChAMP error while lazyloading the latest version ChAMP_2.9.10
... 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 ...
champ written 5 months ago by yura.grabovska10 • updated 5 months ago by Yuan Tian40
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Answer: A: "Seems your IDAT file not from one Array"
... 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.grabovska10
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Comment: C: biomaRt Ensembl ID query returns NA in 'ensembl_gene_id', 'ensembl_transcript_id
... Thanks Mike. This makes sense. I'll implement your suggestion. ...
written 14 months ago by yura.grabovska10
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Comment: C: biomaRt Ensembl ID query returns NA in 'ensembl_gene_id', 'ensembl_transcript_id
... 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.grabovska10
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Comment: C: biomaRt Ensembl ID query returns NA in 'ensembl_gene_id', 'ensembl_transcript_id
... 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.grabovska10
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biomaRt Ensembl ID query returns NA in 'ensembl_gene_id', 'ensembl_transcript_id', etc.
... 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', ...
annotation biomart ensembl written 14 months ago by yura.grabovska10 • updated 14 months ago by Mike Smith2.9k
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Comment: C: conumee error: query intensities not given for all probes.
... 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.grabovska10
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conumee error: query intensities not given for all probes.
... 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 ...
conumee written 14 months ago by yura.grabovska10 • updated 13 months ago by SplittingInfinity30
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Defining metagenes from NMF in methylation array data - next step?
... 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 ...
minfi nmf written 2.6 years ago by yura.grabovska10

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