User: Jack Luo

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Jack Luo340
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Posts by Jack Luo

<prev • 30 results • page 1 of 3 • next >
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question regarding function IMA.methy450PP in IMA package
... Hi, I was trying to process my 27k data, mainly trying to filter the probes with SNPs. After using IMA.methy450R to read in the data, I successfully created an exprmethy450 object, then I followed the instruction load("annot27k_mapped.RData") data@annot = as.matrix(annotout) Then use IMA.methy4 ...
process written 3.7 years ago by Jack Luo340
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where to find a list of housekeeping genes for Affy array (Gene 1.0 ST)
... Not sure whether it's an appropriate question for Bioconductor. Is there a place to find a list of housekeeping genes (identified by Affy)? Thanks, -Jack [[alternative HTML version deleted]] ...
written 4.6 years ago by Jack Luo340 • updated 4.6 years ago by Robert Castelo2.0k
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Comment: C: options on outputing gene expression based on gene level instead of probe set le
... Thanks, Jim. That's very helpful. -Jack On Thu, Mar 7, 2013 at 8:57 AM, James W. MacDonald wrote: > Please don't take things off list. > > On 3/6/2013 7:59 PM, Jack Luo wrote: > >> Gene 1.0 ST. >> > > At this point I guess I need to know what you mean by gene level. ...
written 4.7 years ago by Jack Luo340
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options on outputing gene expression based on gene level instead of probe set level for justRMA
... Hi, I am trying to RMA normalize a bunch of cel files and output the gene expression matrix to gene level (instead of probe set level), is there any option in justRMA that can do this (or any other function that can do this?) I searched the options on justRMA, does not seem to have this option. Th ...
probe written 4.7 years ago by Jack Luo340 • updated 4.7 years ago by Peter Langfelder1.3k
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log transform in RMA normalization
... I am trying to understand the details of the RMA algorithm in terms of log transform. The probe level data obtained from ReadAffy is obviously not log transformed, so in the 3 steps: 1. background subtraction: 2. quantile normalization: 3. median polish summarization. should the algorithm work on ...
normalization probe written 4.8 years ago by Jack Luo340 • updated 4.8 years ago by Ben Bolstad1.2k
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xps installation question
... Hi, I am trying to install the xps package, but it returns some error msg: > source("http://bioconductor.org/biocLite.R") > biocLite("xps") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'xps' package ‘xps ...
xps written 4.8 years ago by Jack Luo340 • updated 4.8 years ago by cstrato3.8k
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Comment: C: question of justRMA on exon array
... Hi James, Thanks for your reply. No, I did not get that idea from anywhere, I am a newbie to Exon array, although I have analyzed a lot of Gene 1.0 ST array. I thought Exon array should be very similar to Gene ST array, that's why I thought justRMA should work for them (since justRMA works fine for ...
written 4.8 years ago by Jack Luo340
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question of justRMA on exon array
... Hi, I am trying to RMA normalize a bunch of exon arrays. I thought this is as easy as what I have done with the gene 1.0 ST array by using justRMA. However, it has the error information: *.CEL does not seem to have cdf information I provided the path of the CDF I downloaded from Affy website, but ...
cdf affy written 4.8 years ago by Jack Luo340 • updated 4.8 years ago by James W. MacDonald45k
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conceptual question about FDR, FDR adjusted p-value and q-value
... Hi, I am a bit confused about the concepts of the 3 things: FDR, FDR adjusted p-value and q-value, which I initially thought I was clear about. Are FDR adjusted p-value the same as q-value? (my understanding is that FDR adjusted p-value = original p-value * number of genes/rank of the gene, is tha ...
qvalue fdr written 4.9 years ago by Jack Luo340 • updated 13 months ago by Gordon Smyth32k
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Comment: C: question regarding using cummeRbund package
... Sure, see below: > sessionInfo() R version 2.15.1 (2012-06-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 at ...
written 5.4 years ago by Jack Luo340

Latest awards to Jack Luo

Student 3.7 years ago, asked a question with at least 3 up-votes. For conceptual question about FDR, FDR adjusted p-value and q-value
Great Question 3.7 years ago, created a question with more than 5,000 views. For conceptual question about FDR, FDR adjusted p-value and q-value
Epic Question 3.7 years ago, created a question with more than 10,000 views. For conceptual question about FDR, FDR adjusted p-value and q-value
Popular Question 3.7 years ago, created a question with more than 1,000 views. For conceptual question about FDR, FDR adjusted p-value and q-value
Popular Question 3.7 years ago, created a question with more than 1,000 views. For conceptual question about FDR, FDR adjusted p-value and q-value

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