User: whyuen

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whyuen0
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Posts by whyuen

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Comment: C: Oligo package: paCalls questions
... Dear James, I have read through the Q&A you were discussing with Juan (https://support.bioconductor.org/p/48218/) and I find you guys are discussing the use of "psdabg" and "dabg" in paCalls().  Am I right to say that rma (target = "core") must be used with "psdabg" in paCalls() while rma(targ ...
written 2.5 years ago by whyuen0
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Comment: C: Oligo package: paCalls questions
... Dear Christian, Can xps package be installed in 64-bit windows? I tried to install the binary package but it complained about the bit-version. Vincent ...
written 2.5 years ago by whyuen0
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Comment: C: Oligo package: paCalls questions
... Dear Christian, I unpacked ROOT from the link above you gave me. Then I put the root file in the defacult directory C:\root. I also changed the environmental variable ROOTSYS:.  And then I tried to install xps in R using these lines. source("http://bioconductor.org/biocLite.R") biocLite("xps") ...
written 2.5 years ago by whyuen0
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Comment: C: Oligo package: paCalls questions
... Hi James, I used the transcript level for analysis before but later when I checked different probesets representing the same gene, I often found significant differences between them in terms of the signals of the probesets. And I'm afraid if I simply analyze the Gene ST array in transcript level, s ...
written 2.5 years ago by whyuen0
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Comment: C: Oligo package: paCalls questions
... Dear Christian, I could only read the README file in Rstudio, and it is written like this:   README File for ROOT Binary Distribution                 ---------------------------------------- Contents ======== Directory root/ : README      - directory containing important information LICENSE     ...
written 2.5 years ago by whyuen0
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Comment: C: Oligo package: paCalls questions
... Hi James, How could I know which probes are background probes? Concerning DABG and PSDABG algorithms, you said DABG analyzes data in probe level while PSDABG analyzes data in probeset level. Actually, I'm not very clear about the differences about probe, probeset, and transcript levels. Could you ...
written 2.5 years ago by whyuen0
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Comment: C: Oligo package: paCalls questions
... Dear Christian, It would be nice if you could help me install xps. I have no idea how to install ROOT =.= Here is my sessioninfo(): > sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8 x64 (build 9200) locale: [1] LC_COLLATE=Chinese ( ...
written 2.5 years ago by whyuen0
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Comment: C: Oligo package: paCalls questions
... Hi Benilton Carvalho, > sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8 x64 (build 9200) locale: [1] LC_COLLATE=Chinese (Traditional)_Hong Kong SAR.950  LC_CTYPE=Chinese (Traditional)_Hong Kong SAR.950    [3] LC_MONETARY=Chinese (Tra ...
written 2.5 years ago by whyuen0
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Comment: C: Oligo package: paCalls questions
... I get your idea, James. That's why I'm now artificially assigning P/M/A to genePS_dabg by writing  genePS_dabg_call = ifelse(genePS_dabg<=0.06,ifelse(genePS_dabg<0.04,"P","M"),"A").  The values used for assigning P/M/A are based on mas5calls function.  But I'm not sure if paCalls uses the s ...
written 2.5 years ago by whyuen0
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Answer: A: Oligo package: paCalls questions
... I am now trying this line: genePS_dabg_call = ifelse(genePS_dabg<=0.06,ifelse(genePS_dabg<0.04,"P","M"),"A") after genePS_dabg <- paCalls(affyRaw,"PSDABG")   The values used for filtering are based on mas5calls function. ...
written 2.5 years ago by whyuen0

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