User: yura.grabovska
yura.grabovska • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- Last seen:
- 11 months, 2 weeks ago
- Joined:
- 3 years ago
- Email:
- y*************@newcastle.ac.uk
Posts by yura.grabovska
<prev
• 9 results •
page 1 of 1 •
next >
0
votes
1
answer
256
views
1
answer
... 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 11 months ago by
yura.grabovska • 20
• updated
11 months ago by
Yuan Tian • 60
1
vote
2
answers
311
views
2
answers
... 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 11 months ago by
yura.grabovska • 20
0
votes
2
answers
483
views
2
answers
... Thanks Mike. This makes sense. I'll implement your suggestion.
...
written 20 months ago by
yura.grabovska • 20
0
votes
2
answers
483
views
2
answers
... 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 20 months ago by
yura.grabovska • 20
0
votes
2
answers
483
views
2
answers
... 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 20 months ago by
yura.grabovska • 20
2
votes
2
answers
483
views
2
answers
... 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 20 months ago by
yura.grabovska • 20
• updated
20 months ago by
Mike Smith • 3.3k
0
votes
2
answers
762
views
2
answers
... 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 20 months ago by
yura.grabovska • 20
7
votes
2
answers
762
views
2
answers
...
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 20 months ago by
yura.grabovska • 20
• updated
19 months ago by
SplittingInfinity • 40
0
votes
0
answers
539
views
0
answers
... 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 3.1 years ago by
yura.grabovska • 20
Latest awards to yura.grabovska
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 16.09
Traffic: 341 users visited in the last hour