User: yura.grabovska

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Posts by yura.grabovska

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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 9 weeks ago by yura.grabovska0
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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 9 weeks ago by yura.grabovska0
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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 9 weeks ago by yura.grabovska0
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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 9 weeks ago by yura.grabovska0 • updated 9 weeks ago by Mike Smith2.0k
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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 10 weeks ago by yura.grabovska0
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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 10 weeks ago by yura.grabovska0 • updated 5 weeks ago by SplittingInfinity0
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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 18 months ago by yura.grabovska0

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