User: Yisong Zhen

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Yisong Zhen200
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Posts by Yisong Zhen

<prev • 23 results • page 2 of 3 • next >
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Comment: C: filtering or not filtering?
... It seems that I have to read carefully the Limma module. I though it will reduce the false positive ( and following step about multiple- testing correction) when filtered out those genes with low expression constantly and genes with low CV. Yisong On Mon, Dec 8, 2008 at 3:48 PM, James MacDonald wrot ...
written 10.9 years ago by Yisong Zhen200
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filtering or not filtering?
... Dear Bioconductor users, Before I performed Limma analysis, should I do non specific filter or not? If we should do filter before Limma step, how do I determine the cut- off for filtering-function? For example, If I use Co-efficient of Variability (CV) as filtering criteria, how should I set the c ...
limma written 10.9 years ago by Yisong Zhen200 • updated 10.9 years ago by Jenny Drnevich1.9k
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Answer: A: Mas5, normalization method, error
... Dear All, I try to use the mas5 to normalize my data. but it failed. However, I can use RMA method to normlize the data. The following is the error message: Loading required package: affyio Loading required package: preprocessCore > raw.data<-ReadAffy(); > mas5.data<-mas5(raw.data); ba ...
written 10.9 years ago by Yisong Zhen200
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Mas5, normalization method, error
... Dear All, I try to use the mas5 to normalize my data. but it failed. However, I can use RMA method to normlize the data. The following is the error message: Loading required package: affyio Loading required package: preprocessCore > raw.data<-ReadAffy(); > mas5.data<-mas5(raw.data); ba ...
written 10.9 years ago by Yisong Zhen200 • updated 10.9 years ago by Wolfgang Huber13k
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p.adj and logFC
... Thanks for your reply. My understanding for the p.adjust from the R help page is that it is adjusted by number of comparison. I mean, if I filter genes (below certain expression threshold) before I carry out multiple testing, the p.adjust would be decreased. But how do we set the threshold for p.a ...
limma written 11.1 years ago by Yisong Zhen200 • updated 11.0 years ago by Sean Davis21k
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p.adj and logFC
... Hello All, I used the following script to find the genes that both have p.adj < 0.05 and logFC < -1 in comparisons (TCdn - TCwt and Tcestw - TCwt). I checked one candidate gene in the normalized expression output (affy_My_data.txt). The first two are TCdn, middle two are TCwt and the last two ...
limma written 11.1 years ago by Yisong Zhen200 • updated 11.1 years ago by James W. MacDonald51k
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arrayQualityMetrics, Outlier
... Dear Bioconductor users, I used arrayQualityMetrics to generate quality report. But, in its summary report, how does it determine array which has potential problem or as being an outlier? I mean, is there some kind of cutoff for MA, Boxplot and heatmap? If it is yes, where can I find them? What i ...
arrayqualitymetrics written 11.1 years ago by Yisong Zhen200 • updated 11.1 years ago by audrey280
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Error in X11(paste("png::", filename, sep = ""),
... Dear Biocondcutors, I used the arrayQualityMetrics package to generate quality control report. But I got this error: Error in X11(paste("png::", filename, sep = ""), width, height, pointsize unable to start device PNG my system information is uname -r 2.6.15-1.2054_FC5smp I think I installed the ...
arrayqualitymetrics written 11.2 years ago by Yisong Zhen200 • updated 11.2 years ago by Henrik Bengtsson2.4k
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library(affyQCReport)-NA(arg1); arrayQualityMetrics-no end
... Dear all, I updated my R and Biocondcutor. I generated the cint06a520380fcdf.qcdef. (1) But when I use the library(affyQCReport), program still said that there had missing values (NA(arg1)). library(limma); library(affy); targets<-readTargets("targets.txt"); data<-ReadAffy(filenames=targets ...
cancer cdf affy simpleaffy affyqcreport affyio arrayqualitymetrics written 11.2 years ago by Yisong Zhen200 • updated 11.2 years ago by rgentleman5.5k
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Comment: C: Quality control;Missing value;installation
... Hi, I updated my R version and Bioconductor. But I met different error, where and how to set up ".qcdef" file? library(affy) Tucson_data <- ReadAffy() library(affyQCReport); # Loads "affy" and "simpleaffy" packages QCReport(Tucson_data, file="ExampleQC.pdf") setQCEnvironment(cdfn) : Could ...
written 11.2 years ago by Yisong Zhen200

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