User: Giovanni Calice

gravatar for Giovanni Calice
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Italy
Last seen:
3 months ago
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4 years, 7 months ago
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Posts by Giovanni Calice

<prev • 78 results • page 1 of 8 • next >
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ChAMP results interpretation
... Hi all, for best interpretation of ChAMP results I was wondering if the frequency plot describe all the possible copy number alterations in all chromosomes and the sampleResult splitted in all samples dataset is the best kind of output to extract the copy number data from CHAMP analysis. Thanks ...
champ written 3 months ago by Giovanni Calice150
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Comment: C: Rgraphviz installation fails
... I'm sorry if I did not describe better in the previous message. Yes, everything works after updating and readjusting the configuration.   Best, Giovanni ...
written 8 months ago by Giovanni Calice150
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Comment: C: DMRcate results cg ID of significant DMR
... Hi Tim, Thanks for response. Best, Giovanni ...
written 8 months ago by Giovanni Calice150
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Comment: C: Rgraphviz installation fails
... Hi Kasper, as I announced I have updated R to the latest version and lightly readjusted my configure command call removing very little for other stuff and anyway linking the rest to have all in capabilities() TRUE/Ok. So Rgraphviz is intalled correctly to the latest version 2.22.0 . Best, Giov ...
written 8 months ago by Giovanni Calice150
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Comment: C: IlluminaHumanMethylationEPIC array nSNPsRead and MethylSet probes
... Dear Kasper, in fact for the 450k it never happened this issue. Thanks for response, Best Giovanni ...
written 8 months ago by Giovanni Calice150
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IlluminaHumanMethylationEPIC array nSNPsRead and MethylSet probes
... Hi all, I'm processing some new IlluminaHumanMethylationEPIC arrays but I obtained different reading number of SNPs (nSNPsRead) in the IDAT files, 1051815, compared to the ones I've always usually got from IlluminaHumanMethylationEPIC array, 1052641 . # # Old chip file # old <- readIDAT("/wor ...
minfi illuminaio illuminahumanmethylationepicmanifest written 8 months ago by Giovanni Calice150 • updated 8 months ago by Kasper Daniel Hansen6.4k
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limma results more probes for same gene
... Hi all, I've processed some differential analysis by limma on Illumina Gene Expression Array, and I'm working to intersect the results. I am of the opinion that the correct choice to intersect is by Probe Id (unique field) and I usually did so. Now I was wondering again if you want to intersect by ...
limma written 12 months ago by Giovanni Calice150
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Comment: C: Rgraphviz installation fails
... Hi Kasper, Ok I've already checked my env and mentioned the only env var that refers to R. There's something to reset in configure command when I installed R; what I was wondering is why the compilation is successfull for all other packages . Anyway I'll reset/reinstall R (also because I want to ...
written 13 months ago by Giovanni Calice150
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Comment: C: Rgraphviz installation fails
... Sorry, How can I fix/force the lib path before run Rgraphviz installation? ...
written 13 months ago by Giovanni Calice150
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Comment: C: Rgraphviz installation fails
... Yes, I disinstalled the graphviz version 2.28.0; this was just another test to verify if the Rgraphviz installation was successful. Anyway there isn't any configuration file (like .R/Makevars) and the only env var set, which concerns R, is R_LIBS_USER=/usr/local/lib64/R/library_Bioc that I set f ...
written 13 months ago by Giovanni Calice150

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Popular Question 15 months ago, created a question with more than 1,000 views. For bumphunter DMRs difficulties

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