User: Stephen Piccolo

gravatar for Stephen Piccolo
Reputation:
510
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Location:
United States
Twitter:
stevepiccolo
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Last seen:
2 weeks, 5 days ago
Joined:
9 years, 9 months ago
Email:
s**************@byu.edu

Posts by Stephen Piccolo

<prev • 102 results • page 1 of 11 • next >
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Comment: C: Transcript-level SCAN.UPC preprocessing for Affymetrix HTA 2.0 arrays
... Thanks for the detailed response. There's no reason that SCAN.UPC can't handle these conventional transcript-level mappings. I haven't come across anyone who needed this, though. Have you? ...
written 19 days ago by Stephen Piccolo510
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Comment: C: Transcript-level SCAN.UPC preprocessing for Affymetrix HTA 2.0 arrays
... Here's a link to the BrainArray site: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp#v22 ...
written 19 days ago by Stephen Piccolo510
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Answer: A: Transcript-level SCAN.UPC preprocessing for Affymetrix HTA 2.0 arrays
... I apologize for my delay in replying. I may be misunderstanding what you want to do, but you should be able to solve this by using BrainArray annotations. You can read about this in the SCAN.UPC vignette. BrainArray now has annotations for the HTA 2.0 arrays. You can use the probeSummaryPackage arg ...
written 19 days ago by Stephen Piccolo510
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Comment: C: Transcript-level SCAN.UPC preprocessing for Affymetrix HTA 2.0 arrays
... I will have to go into the code to remember why that is the case and see if there is a better way to handle it. It might take me a few days (due to the US holidays) to get to it. Does hta20transcriptcluster.db have probe information? ...
written 4 weeks ago by Stephen Piccolo510
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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 9 weeks ago by Stephen Piccolo510
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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 9 weeks ago by Stephen Piccolo510
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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 4 months ago by Stephen Piccolo510
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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 4 months ago by Stephen Piccolo510
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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 10 months ago by Stephen Piccolo510
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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 11 months ago by Stephen Piccolo510

Latest awards to Stephen Piccolo

Scholar 11 months ago, created an answer that has been accepted. For A: normalization with mas5
Scholar 2.5 years ago, created an answer that has been accepted. For A: normalization with mas5
Teacher 2.8 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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