User: Pedro López Romero

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Posts by Pedro López Romero

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Comment: C: AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G44
... Hi Neel and Richard, Thanks for your patience. I have slitghtly modified some code in the package, basically related to the way read.maimages is used. I have eliminated the use of the "chr_coord" column in some of the output files which it was what it was causing problems. Before these changes a ...
written 9.4 years ago by Pedro López Romero360
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Comment: C: AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G44
... Thanks Neel, I am working on your data, I know where the problem is. I have to modify (or even write a new function) to read the data in such a way that it is more flexible to the different data formats. I will let you know when I have this ready. p.- De: Neel Aluru [mailto:naluru@whoi.e ...
written 9.4 years ago by Pedro López Romero360
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Answer: A: Error message with rmaMicroRna on mouse data in AgiMicroRNA
... Thanks Richard, I am looking at the headings of your files, and it seems that the "chr_coord" it?s not present. This might not be an issue, but if the FE 10 version (or mouse data) don?t provide this column, I will have to modify the function that reads the data. Could you send me one of your files ...
written 9.4 years ago by Pedro López Romero360
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Comment: C: AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G44
... Thanks for your patience Neel, could you send me one of the files you are using, it would help me a lot working directly on the same data you are using. p.- De: Neel Aluru [mailto:naluru@whoi.edu] Enviado el: Thursday, June 17, 2010 1:49 PM Para: Pedro López Romero; bio c bioconductor Asun ...
written 9.4 years ago by Pedro López Romero360
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Answer: A: AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G44
... Hi Neel, I think your problem with the filtering function, is not the filtering itself but when the function tries to write an output. I am modifying this, so the user can choose whether or not they want to have an output file in the filtering step. In the meantime, can you tell me what you have ...
written 9.4 years ago by Pedro López Romero360
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Answer: A: Error message with rmaMicroRna on mouse data in AgiMicroRNA
... Dear Richard, AgiMicroRna has not been tested on mouse data, something that I?m just doing right now. It seems that I am having problems myself loading the data into R. What version of Agilent Feature Extraction are you using?. The people that usually provide me with the scanned data files told me ...
written 9.4 years ago by Pedro López Romero360
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Comment: C: AgiMicroRna - FilterMicroRna question
... Hi, I don?t understand why you are using ddaux=read.maimages and then dd=readMicroRnaAFE(targets.micro, verbose=TRUE). If readMicroRnaAFE is giving you a problem with the selection of the columns (this function selects dd$genes=ddaux$genes[,c(4,5,6)], that should correspond to "ControlType" "Probe ...
written 9.4 years ago by Pedro López Romero360
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Comment: C: AgiMicroRna - FilterMicroRna question
... Hi Neel, Try to use readMicroRnaAFE(targets,verbose=TRUE) to load your data into R instead of calling read.maimages() by yourself. This will solve your problem Cheers p.- -----Mensaje original----- De: Neel Aluru [mailto:naluru at whoi.edu] Enviado el: Tuesday, June 01, 2010 7:34 PM Para: Martin ...
written 9.5 years ago by Pedro López Romero360
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Answer: A: readMicroRnaAFE function in AgiMicroR package
... Hi Heyi, readMicroRnaAFE uses the read.maimages function from limma. You can edit readMicroRnaAFE and remove the {ChrCoord="chr_coord"} in the “other.columns” list arguments. However, if you want to use RMA you will need the “gMeanSignal”. If you don´t have the gMeanSignal, change that a ...
written 9.7 years ago by Pedro López Romero360
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Answer: A: Analysing Agilent microarray data
... Hi, With Agi4x44PreProcess you can use either the Raw Mean Signal and do some background correction, or you can use the ProcessedSignal and go straight to the normalization between arrays. What sort of signal you use it´s up to you. Usually, I take the Raw Mean Signal and apply the half BG correcti ...
written 10.8 years ago by Pedro López Romero360

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