User: Stephen Piccolo

gravatar for Stephen Piccolo
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500
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United States
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stevepiccolo
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3 days, 19 hours ago
Joined:
9 years, 7 months ago
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Posts by Stephen Piccolo

<prev • 98 results • page 1 of 10 • next >
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Comment: C: Normalization of multiple HTA 2.0 arays using SCAN.UPC
... SCAN is slower and uses more memory than some other methods. But it explicitly accounts for the probe sequences, thus adjusting for probe-sequence composition on a single-sample basis, unlike other methods. If speed is a concern, you can try the SCANfast function, which should give similar results a ...
written 6 days ago by Stephen Piccolo500
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Comment: C: Normalization of multiple HTA 2.0 arays using SCAN.UPC
... What do you get if you use the following on the last line of your code rather than what you currently have? normalized = SCAN(celFilePattern) ...
written 7 days ago by Stephen Piccolo500
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Answer: A: ParseMetaFromGtfFile() from SCAN.UPC package fails to produce annotation file
... Thanks for letting me know about this. Some of the information that is often stored in the second column was stored in a different location within the file. I believe I have fixed the problem. I'll post it as soon as I can to the devel server. But for now, send me an email, and I'll send you the fix ...
written 10 weeks ago by Stephen Piccolo500
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Comment: C: ParseMetaFromGtfFile() from SCAN.UPC package fails to produce annotation file
... I'll look into this and get back to you. ...
written 10 weeks ago by Stephen Piccolo500
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Comment: C: Problem about use of tcga rna-seq rsem gene results for regularized cox regressi
... If you want a kallisto-processed version of the TCGA RNA-Seq data, you might consider my paper here: http://www.nature.com/articles/srep39259 ...
written 8 months ago by Stephen Piccolo500
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Answer: A: UPC transposes output data
... I talked to Guus offline. It turned out the inconsistent behavior was likely due to using as.matrix() to extract UPC values from the ExpressionSet object rather than exprs(). exp <- exprs(UPC_RNASeq("prova.txt", ignoreZeroes = T)) ...
written 9 months ago by Stephen Piccolo500
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Comment: C: UPC transposes output data
... Thanks for your question. I'll take a look into it.  ...
written 9 months ago by Stephen Piccolo500
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Comment: C: About the best use of frma for several GEO Series
... Is the use of fRMA a requirement for your study? If not, you might consider using our SCAN.UPC package for this. Nothing against fRMA, but with our package you can specify the GSE identifier directly when you invoke the SCAN() function. This will download and normalize the data in one step. The conc ...
written 11 months ago by Stephen Piccolo500
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Comment: C: Getting a flat metadata table from the XML files in TCGA: is it feasible?
... I don't know if this helps, but we created an tab-separated version of much of the TCGA clinical data for this project: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944 ...
written 12 months ago by Stephen Piccolo500
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Comment: C: Question about Agilent microarray data measurement
... Or I guess you could instead say "on" = "Present" and "off" = "Absent" if you prefer that terminology. ...
written 12 months ago by Stephen Piccolo500

Latest awards to Stephen Piccolo

Scholar 9 months ago, created an answer that has been accepted. For A: normalization with mas5
Scholar 2.4 years ago, created an answer that has been accepted. For A: normalization with mas5
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Can I feed TCGA normalized count data to EdgeR for differential gene expression

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