User: Pedro Lopez-Romero

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Posts by Pedro Lopez-Romero

<prev • 12 results • page 1 of 2 • next >
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AgiMicroRna problem
... Hi Pablo, The function "read.maimages" is no longer used by AgimicroRna. "read.maimages" creates an object of class RGList with element names: R, Rb, G, Gb, etc ..., that are proper for two-channel arrays. To make the names more intuitive for the analysis of microRna arrays, I have introduced some ...
annotation microrna agimicrorna written 8.3 years ago by Pedro Lopez-Romero120 • updated 8.3 years ago by Paulo Nuin200
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Comment: C: Normalisation of Agilent microRNA arrays using inbuilt controls?
... Hi, in AgiMicroRNa we don´t advocate for any particular method of normalization. We have included scale, quantile and RMA and we let the user decide what might best method for them. You may even want to try some other methods that are not currently implemented in the package. Recently we have publi ...
written 9.3 years ago by Pedro Lopez-Romero120
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Comment: C: cvArray error from AgiMicroRna package
... Hi, the cvArray function uses "which(duplicated(ddDUP$genes$ProbeName)==TRUE)" to get the duplicated Probes. If instead of having "ProbeName" you have "ProbeUID" the function is not going to work. The readMicroRnaAFE() uses read.maimages() from limma, and then we select what columns are retained in ...
written 9.3 years ago by Pedro Lopez-Romero120
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Agi4x44PreProcess 1.4.0 question: use of genes.rpt.agi() and Gene Sets
... Hi Massimo, the intention of the genes.rpt.agi function is to detect which genes are interrogated by different probes at different chromosomal location. I think it could be somewhat dangerous to summarize the expression values of those genes in the Agilent chips, sometimes you can find the same gen ...
hgug4112a probe limma agi4x44preprocess written 9.4 years ago by Pedro Lopez-Romero120
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Answer: A: Error message of read.AgilentFE() using package Agi4x44PreProcess
... Hi, As I understand, you want to read the files that you have in your target file, '1.txt'. Apparently, when you use 'data(targets)' the target file that is included in the package as an example is loaded and substitute your targets variable, then the read.AgilentFE() function attempts to read the f ...
written 9.9 years ago by Pedro Lopez-Romero120
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microRNA Agilent normalization
... Hi all, I am using the microRNA Agilent platform to conduct a differential expression analysis. Does anyone know what are the processing protocol that is recommended by the Agilent manufacturer? I think that we should use the Total Gene Signal (TGS), but, does Agilent recommend any sort of normal ...
normalization microrna written 10.0 years ago by Pedro Lopez-Romero120
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Answer: A: read.targets() in the Agi4x44PreProcess package
... Hi Massimo, just try > targets=cbind(targets,targets$FileName) > targets[,1]=rownames(targets) > colnames(targets)[4]='FileName2' > targets p.- On Thu, May 7, 2009 at 9:31 AM, Massimo Pinto wrote: > Greetings all, > please consider my targets file > > FileName ...
written 10.1 years ago by Pedro Lopez-Romero120
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Comment: C: Problem loading data for Agi4x44PreProcess
... Hi, First you need to read the target file targets=read.targets(infile='target.file.name.txt') and then your data files dd=read.AgilentFE(targets,makePLOT=FALSE) *this* reads the data files into R and and creates an *RGList* object that contains the following variables: the scanned mean raw si ...
written 10.1 years ago by Pedro Lopez-Romero120
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Comment: C: Agi4x44PreProcess: filtration of probes using filter.probes() returns an empty R
... Hi again Massimo, please, show me as well what you have in your targets$GErep p.- On Mon, Apr 27, 2009 at 4:01 PM, Pedro Lopez-Romero < plromero1.bioc@gmail.com> wrote: > Hi Massimo, can you show me what you have in targets$Treatment? > > p.- > > On Mon, Apr 27, 2009 at 7: ...
written 10.1 years ago by Pedro Lopez-Romero120
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Answer: A: Agi4x44PreProcess: filtration of probes using filter.probes() returns an empty R
... Hi Massimo, can you show me what you have in targets$Treatment? p.- On Mon, Apr 27, 2009 at 7:17 AM, Massimo Pinto wrote: > I am reposting this only because, from the web archive of this list, it > appears that > An embedded and charset-unspecified text was scrubbed... > Name: not av ...
written 10.1 years ago by Pedro Lopez-Romero120

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