User: Alison Ziesel

gravatar for Alison Ziesel
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Posts by Alison Ziesel

<prev • 12 results • page 1 of 2 • next >
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Comment: C: oposSOM error and annotation question
... Attempting the same R code in a different work environment:   [2015-07-18 17:29:40][INFO] Started: Sat 18 Jul 2015 05:29:40 PM [2015-07-18 17:29:40][INFO] Setting: Mendoza All [2015-07-18 17:29:40][INFO] 1SOM Dim: 20 [2015-07-18 17:29:40][INFO] 2SOM Dim: 20 [2015-07-18 17:29:51][INFO] Load Annotat ...
written 4.0 years ago by Alison Ziesel60
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Comment: C: oposSOM error and annotation question
... Hello Henry, Thank you so much for your quick response! I've come back to it with your suggestions, and now get the following error (R code included): > eset.matrix <- as.matrix(eset) > > env <- opossom.new(list(dataset.name="M All", + error.model="all.samples", + dim.1stLvlSom=20, ...
written 4.0 years ago by Alison Ziesel60
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Comment: C: oposSOM error and annotation question
... And here's that SessionInfo. > sessionInfo() R version 3.1.3 (2015-03-09) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.9.5 (Mavericks) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats4    parallel  stats     grap ...
written 4.1 years ago by Alison Ziesel60
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oposSOM error and annotation question
... I've just started with the oposSOM package to identify key genes in an array study I'm analyzing for a collaborator, and I have two questions about the package. Below is my R code and the error message, along with everything oposSOM reported during its workflow. "Eset" is an expression set generated ...
software error written 4.1 years ago by Alison Ziesel60 • updated 4.1 years ago by wirth0
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Comment: C: HuGene 2.0 ST CDF files and xps
... Thank you for your swift reply! I had found the .pgf, .clf, and .csv files earlier, but was trying to use import.expr.scheme rather than import.exon.scheme as described in the script4schemes.R file. Thank you so much for clearing this up for me, I'm very grateful!   alison ...
written 4.8 years ago by Alison Ziesel60
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HuGene 2.0 ST CDF files and xps
... Hello all, I had written to the list earlier this month regarding a function of the oligo package ("Oligo package: paCalls question"), and mentioned I had had difficulty getting an alternate package, xps, installed. After setting the problem aside for a period, I've since been able to correctly com ...
xps hugene20 written 4.8 years ago by Alison Ziesel60 • updated 4.8 years ago by cstrato3.9k
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Comment: C: Oligo package: paCalls question
... Hello again Jim, I adapted that second segment of code (poorly) from the page you had linked earlier, the August 2014 commentary from Dr. Stratowa. I confess I was reaching a bit with it. Thank you for clarifying where I was going wrong; I was operating on some very poor assumptions, it seems. I h ...
written 4.9 years ago by Alison Ziesel60
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Comment: C: Oligo package: paCalls question
... Hello Jim, Thanks so much for the speedy reply, I appreciate it. At this point in my workflow I haven?t yet performed RMA. That sounds like mistake #1 on my part. I too had found that post by Dr. Stratowa but I confess I didn?t entirely understand it. I am willing to exclude absent probes at the ...
written 4.9 years ago by Alison Ziesel60
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Oligo package: paCalls question
... Hello all, I?ve got very basic familiarity with the oligo package, but I?ve ran into a bit of trouble with the paCalls function. I?d like to restrict the probes in my eSet object to only those called present. Here?s what I?ve done thus far: >library(?oligo?) >library("pd.hugene.2.0.st?) > ...
oligo written 4.9 years ago by Alison Ziesel60 • updated 4.9 years ago by James W. MacDonald50k
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Answer: A: lumi question (About BeadStudio output columns)
... Hello Dr. Du, Thank you so much for your quick reply. One of the files provided to me by our core facility did include BEAD_STDERR (as well as the other columns you mentioned), and I got this error when I attempted to load that file: > probe_file <- lumiR("Probe.txt", lib = "lumiRatV1") Er ...
written 11.0 years ago by Alison Ziesel60

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Popular Question 3.8 years ago, created a question with more than 1,000 views. For HuGene 2.0 ST CDF files and xps

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