User: Gustavo Fernández Bayón

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Posts by Gustavo Fernández Bayón

<prev • 45 results • page 1 of 5 • next >
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Repetitive motifs on Illumina 450k derived sequences
... Hi everybody, (First of all, I would like to admit that I am posting this question here two days after posting it at Biostars. The latter seems to be quite inactive, at least with respect to the subject under question, and I thought it could be a good idea to share this with the R/Bioc community.) ...
illumina 450k meme motifs written 2.8 years ago by Gustavo Fernández Bayón440
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Answer: A: Questions on Combat in methylation data Thank you for your help
... Hi, I have not been able to see the attached file. However, the high number of batches sometimes indicates that we have failed to indicate the continuous covariates (with the numCovs argument), thus taking a continuous variable as a factor... Could it be this? Regards, Gus El 09/12/13 15:54, Joh ...
written 4.9 years ago by Gustavo Fernández Bayón440
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Limma for DNA methylation arrays?
... Hi Gordon, Tim, First of all, let me thank you for your answers. They have been very helpful. Using Gordon's recommendations (paired design, robust method and eBayes with a trend for the prior), I've been able to extract a subset of differentially methylated probes big enough for us to continue wit ...
normalization probe limma minfi written 4.9 years ago by Gustavo Fernández Bayón440
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Limma, blocking, robust methods, and paired samples question
... Hello everybody. I am experiencing some problems with a methylation microarray experiment I am trying to analyze and, although I am able to get results to some extent, I am suspicious about them and would like to know if I am doing things correctly. We have 12 samples. Each sample is built on DNA ...
microarray probe written 4.9 years ago by Gustavo Fernández Bayón440 • updated 4.9 years ago by Gordon Smyth35k
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Answer: A: minfi: Problem with GenomicMethylSet
... Hi everybody. Just providing another bit of information on the previous question. I have noticed that the constructor for ShallowSimpleListAssays in the GenomicRanges package has changed to a new two-step, faster, method. I think that might be the reason behind the GenomicMethylSet misbehaviour I f ...
written 5.4 years ago by Gustavo Fernández Bayón440
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minfi: Problem with GenomicMethylSet
... Hi everybody. After upgrading to R3.0 and Bioc 2.13, some of my scripts broke. Currently I have a problem that I'll try to reproduce here with a minimal scenario: I have a MethylSet produced by preprocessSWAN. > mset MethylSet (storageMode: lockedEnvironment) assayData: 485512 features, 20 sa ...
annotation minfi written 5.4 years ago by Gustavo Fernández Bayón440
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Detecting significant trends in variability
... Hi everybody, I have a question related to the analysis of methylation microarray data. At first, I asked it on Biostar (here http://www.biostars.org/p/64405/#64521) and somebody there suggested me to put it also here. The question is: "[..] I am currently working on a DNA methylation microarray a ...
microarray preprocessing probe minfi written 5.7 years ago by Gustavo Fernández Bayón440
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Answer: A: Rtracklayer and track/table names
... Hi again. I have just found a way to overcome my previous problem. I am posting it here, in case somebody needs it. Went to the UCSC Table Browser, and found the corresponding track and table name in the selection boxes. Track I was searching was 'NKI LADs (Tig3)' and table name was 'laminB1Lads'. ...
written 5.7 years ago by Gustavo Fernández Bayón440
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Rtracklayer and track/table names
... Hi everybody. I am currently using rtracklayer a lot, but I am experiencing some problems with the names of the trackas and tables. For example, I wanted to query the NKI Lads track, which is a hg18 liftover available from the UCSC browser. I do the following: > s <- browserSession() > ...
rtracklayer written 5.7 years ago by Gustavo Fernández Bayón440
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Comment: C: rtracklayer: small problem
... Hi Michael. Thank you very much. Now it makes perfect sense. I was using getTable(), but I think it will be better to change and keep consistency across all of my code. Thank you again. Regards, Gus On 16/01/13 13:13, Michael Lawrence wrote: > Hi Gustavo, > > UCSC stores its ranges as 0 ...
written 5.8 years ago by Gustavo Fernández Bayón440

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Popular Question 2.7 years ago, created a question with more than 1,000 views. For Limma for DNA methylation arrays?

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