User: José LÓPEZ

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José LÓPEZ110
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Posts by José LÓPEZ

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Comment: C: vsn preprocess with oligo package
... Ooops. Sorry for the question. I use to check CEL images and to further analyze quality with arrayQualityMetrics but yes, I didn't realize that the GeneFeatureSet was indicating the total number of probes in the array. Thank you again for your kind help, Best, Jose El ene 11, 2013, a las 6:46 ...
written 6.7 years ago by José LÓPEZ110
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Comment: C: vsn preprocess with oligo package
... Hi, I have one more question. The GeneFeatureSet has 1102500 features while the vsn2 is done on 899636 features no matter whether target in pm is "core" (default method) or "probeset". Why vsn2 does not use all the features? Is that correct/normal? After sumarization, as expected, I have 35556 feat ...
written 6.7 years ago by José LÓPEZ110
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Comment: C: vsn preprocess with oligo package
... Yes, the exprs() did the job and it is allowing me to combine vsn with oligo and Gene ST arrays. Thank you again for your kind help, Best, Jose > library(limma) > library(oligo) > Data=read.celfiles(list.celfiles()) Loading required package: pd.mogene.1.0.st.v1 Loading required packag ...
written 6.7 years ago by José LÓPEZ110
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Comment: C: vsn preprocess with oligo package
... Dear Jim, Thank you for the advise on the background correction step. I already tryed before the whole Benilton's code but it doesn't work at the following step. > pm(raw) <- pmVSN Error: object 'pmVSN' not found May I ask you what this step is doing? Does it replace the pm matrix in the ra ...
written 6.7 years ago by José LÓPEZ110
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vsn preprocess with oligo package
... Dear Benilton, I am using oligo for Mouse Gene 1.0ST arrays. In addition to RMA, I would also like to pre-process with vsn. I have seen previous threads related to this question in the past, (https://stat.ethz.ch/pipermail/bioconductor/2010-January/031100.html, https://stat.ethz.ch/pipermail/biocon ...
vsn oligo oligoclasses written 6.7 years ago by José LÓPEZ110 • updated 6.7 years ago by James W. MacDonald51k
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Comment: C: error preProcessGeneST ArrayTools (R 2.15.2, BioC 2.11)
... Hi Jim, Ok, thank you very much for your input. Makes much more sense to filter after variability estimation. Thanks again for your suggestion. Jose El dic 20, 2012, a las 11:18 p.m., James W. MacDonald escribi?: > Hi Jose, > > On 12/20/2012 4:55 PM, Jos? L?pez wrote: >> Hi Jim, & ...
written 6.8 years ago by José LÓPEZ110
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Comment: C: error preProcessGeneST ArrayTools (R 2.15.2, BioC 2.11)
... Hi Jim, Thank you for your quick reply and your useful explanation. In fact, I was using the function to subset the eset since I didn?t know other way to do it (before). By the way, I would like to know your opinion about whether is a good option to filter controls before doing moderate t-statisti ...
written 6.8 years ago by José LÓPEZ110
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error preProcessGeneST ArrayTools (R 2.15.2, BioC 2.11)
... Dear all, I was trying to use preProcessGeneST ArrayTools to get rid of control probes in Mouse Gene 1.0ST arrays, but it dosent work in last R/BioC version. It was working perfectly in previous R/BioC version. Do I downgrade to previous version to continue to use the ArrayTools package? It is pos ...
annotation go arraytools written 6.8 years ago by José LÓPEZ110 • updated 6.8 years ago by James W. MacDonald51k
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ChipPeakAnno / GRanges isolate peaks that do NOT overlap
... Dear Julie, I am using findOverlappingPeaks and makeVennDiagram to compare 2 set of peaks (A and B). I get overlapping peaks of A with B ($Peaks1withOverlaps) (9992 see below). My question is to how can I get those peaks specific to A (13268) and those specific to B (2640)? I also tried with sub ...
go gui bsgenome written 7.1 years ago by José LÓPEZ110 • updated 7.1 years ago by Julie Zhu4.0k
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Comment: C: ChipPeakAnno: 4-way venn diagram
... Dear Julie, Sorry for my mistake with BioC and ChIPpeakAnno version numbers, Current version of ChipPeakAnno (2.4.0) does 4-way venn diagrams truly nice. Thank you for your quick answer and for such a nice tool, Best, Jose El ago 8, 2012, a las 7:00 p.m., Zhu, Lihua (Julie) escribi?: > Jose ...
written 7.1 years ago by José LÓPEZ110

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Popular Question 6.7 years ago, created a question with more than 1,000 views. For ChipPeakAnno / GRanges isolate peaks that do NOT overlap

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