User: Pan Du

gravatar for Pan Du
Pan Du80
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80
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New User
Location:
United States
Last seen:
4 years, 5 months ago
Joined:
8 years, 5 months ago
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Posts by Pan Du

<prev • 14 results • page 1 of 2 • next >
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Answer: A: Problems importing Illumina raw data with lumi R package
... Hi This question was asked and answered several times. Basically I believe your data missing the STDEV or STDERR columns (depends on you BeadStudio version), which are required by LumiBatch class. When your data missing these columns, the lumiR function will output the ExpressionSet object instead o ...
written 4.2 years ago by Pan Du80
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Answer: A: lumiR.batch fails after upgrade to R v3.2.0 and lumi v2.20.0
... Hi Jeremy Thanks for sending the test data. As you said, it runs well for old versions, but has problem for the new R and Bioc release. After I checked the code, I found the error was caused by capture.output of match.call returns (for the purpose of tracking operation history of the data). I guess ...
written 4.3 years ago by Pan Du80
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Answer: A: lumiR.batch fails after upgrade to R v3.2.0 and lumi v2.20.0
... Hi Jeremy I didn't remember I changed the lumiR.batch function. Can you send me some example data to repeat your error? You can send it to my personal email: dupan.mail (at) gmail. Thanks! Pan On Mon, Apr 20, 2015 at 11:55 AM, Jeremy Martinson [bioc] < noreply@bioconductor.org> wrote: > ...
written 4.3 years ago by Pan Du80
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Comment: C: Understanding methyAnalysis Results
... Yes. t-score is the test statistic from the t-test. On Fri, Mar 6, 2015 at 2:10 AM, andrew.j.skelton73 [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User andrew.j.skelton73 <https: support.bioconductor.org="" u="" ...
written 4.5 years ago by Pan Du80
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Answer: A: methyAnalysis M values and Beta Values
... Yes. Beta = 2^M/(2^M + 1). But for the difference between M-values, there is no direct way to convert as the difference between Beta-values. You have to convert the M-values as Beta values first and then calculate the difference. On Fri, Mar 6, 2015 at 2:59 AM, andrew.j.skelton73 [bioc] < norepl ...
written 4.5 years ago by Pan Du80
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Comment: C: Removing samples from S4 object (in lumi)
... Hi Chi Levi pointed out the problem. And I have fixed the bug in the developing version of lumi. As a temporary solution, please use lumiExpr[, -which(badsamp)] for subsetting. Pan On Thu, Mar 5, 2015 at 1:03 PM, Chi Hong [bioc] <noreply@bioconductor.org> wrote: > Activity on a post y ...
written 4.5 years ago by Pan Du80
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Comment: C: Removing samples from S4 object (in lumi)
... Thanks! Levi I have just fixed the bug and submit the change to lumi 2.19.1. Before the fix to be released, as a temporary solution, users can first convert the logical values as numeric index using which function and then do subsetting. Pan On Thu, Mar 5, 2015 at 11:37 AM, Levi Waldron [bioc] & ...
written 4.5 years ago by Pan Du80
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Answer: A: Removing samples from S4 object (in lumi)
... As the error message shows, please check the colnames of controlData. If they are inconsistent with the sampleNames of lumiExpr, just rename them and try again. Pan On Thu, Mar 5, 2015 at 9:54 AM, Chi Hong [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on ...
written 4.5 years ago by Pan Du80
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Answer: A: Understanding methyAnalysis Results
... Hi Andrew The DMR analysis of detectDMR.slideWin is based on the locally smoothed methylation data. That's why the estimated Difference you get (based on smoothed data) is different from the difference between the original probes (without smoothing). The tscore column basically is the calculated t- ...
written 4.5 years ago by Pan Du80
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Answer: A: dealing with negative values in illumina
... Hi Prasad If you only have processed Illumina GEO data and the maximum of expression value is larger than 100, then I guess the negative values were caused by background correction. Also most negative values should be close to zero, or else the data may have some problem. If you don't want to thr ...
written 8.4 years ago by Pan Du80

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