User: Lavorgna Giovanni

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Posts by Lavorgna Giovanni

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Using up- and down-regulated genes in a signature with SigCheck
... I would like to use the SigCheck package to check the effect of a gene signature on phenotypic data of a dataset of mine. However, I am not sure I understood how to indicate which one are the genes that are over-expressed and those that are instead underexpressedcin in my signature. Could you please ...
sigcheck written 8 months ago by Lavorgna Giovanni80 • updated 8 months ago by Rory Stark2.9k
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Exporting in XPS
... Dear all, before applying any filter to Exon data, I would like to export them to a text file as transcripts, i.e, I have RMAed my data using the following command following the code coming along with the package: rma.tc.core <- rma(data.exon, "MixExonRMAcore", filedir=outdir, tmpdir="", backgr ...
written 7.3 years ago by Lavorgna Giovanni80 • updated 7.3 years ago by cstrato3.9k
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Answer: A: R: R: R: R: Probe-level analysis of exon arrays using xps
... Dear Christian, many thanks for your further advice on this matter. Next few days, I will try your workarounds and I'll let you know how things go. Once again, thanks for your support even late at nights :-) Giovanni ----------------------------------------------------------- Giovanni Lavorgna D ...
written 8.2 years ago by Lavorgna Giovanni80
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I: R: R: R: Probe-level analysis of exon arrays using xps
... Dear Christian, thanks for your answer. Sorry for not being clear in my previous massage. I'll try to clarify things a little bit more. The following script running in a R session ( xps_1.12.1 + root 5.27/04) crashes after finishing the rma step, i.e., it completes the line: rma.ps.core <- rma( ...
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Comment: C: R: R: Probe-level analysis of exon arrays using xps
... Dear Christian, many thanks for your answer and for clarifying matters with the different ROOT releases. Yes, before I was using root_v5.26.00 without patch and I can confirm you that the pipeline you designed without the median-polish sumamrization ran without problems. However, I tried also the ...
written 8.2 years ago by Lavorgna Giovanni80
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R: R: Probe-level analysis of exon arrays using xps
... Dear Christian, I had the chance to use the whole pipeline you designed and it performed very well. Basically, I got the probe intensities I was looking using the whole 185 array dataset. However, if you don't mind, I have a couple of more questions: 1) I would need to check also the probe intens ...
annotation normalization breast prostate probe category xps written 8.2 years ago by Lavorgna Giovanni80 • updated 8.2 years ago by cstrato3.9k
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Comment: C: Probe-level analysis of exon arrays using xps
... Dear Christian, many thanks for your detailed explanations and the new xps development version. I couldn't hope for a better support and this is exactly what I was looking for. I am currently away from the lab with a slow internet connection and I couldn't test the whole pipeline you designed. How ...
written 8.2 years ago by Lavorgna Giovanni80
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Comment: C: Probe-level analysis of exon arrays using xps
... Dear Cristian, many thanks for your prompt answer. In my case, once I have the probe intensities, I would like to do the following two preliminary steps: a) Remove probes that hybridize to multiple loci in the genome. b) Remove probes that show a correlation coefficient below a certain threshold. Th ...
written 8.2 years ago by Lavorgna Giovanni80
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Probe-level analysis of exon arrays using xps
... As you guys know, there is a growing evidence showing that a probe- level analysis (as opposed to a probeset-level or a gene-level analysis) could be useful in analyzing Exon arrays. I am currently analyzing several human exon chips (185!) on a 4 GB machine and I am using the xps package. I would ...
probe xps written 8.2 years ago by Lavorgna Giovanni80 • updated 8.2 years ago by cstrato3.9k

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