User: Wang, Jixin

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Wang, Jixin130
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Posts by Wang, Jixin

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Comment: C: LIMMA Sort problem
... Hi Jim, Thanks a lot for the kind help. I had solved the problem by using of sort=?none? option. Best Regards, Wang ----- Original Message ----- From: "James W. MacDonald" To: "Jixin Wang" Cc: bioconductor at stat.math.ethz.ch Sent: Tuesday, November 4, 2008 12:15:22 PM GMT -06:00 US/Canada Cent ...
written 9.8 years ago by Wang, Jixin130
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Comment: C: LIMMA Sort problem
... Hi Jenny, Thanks a lot. I appreciate your kind help. I really need to make efforts on learning R. Best Regards, Wang ----- Original Message ----- From: "Jenny Drnevich" To: "Jixin Wang" , bioconductor at stat.math.ethz.ch Sent: Tuesday, November 4, 2008 12:55:22 PM GMT -06:00 US/Canada Central Su ...
written 9.8 years ago by Wang, Jixin130
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LIMMA Sort problem
... Dear All, I have one question about the consistence between topTable output with GPR file. In my GPR file, I have several columns containing the annotation information associated with the probes. Can I get differential expression gene list according to GPR file without sort so that I can copy and pa ...
limma written 9.8 years ago by Wang, Jixin130 • updated 9.8 years ago by Jenny Drnevich1.9k
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Comment: C: limma2annaffy output and heatmap questions
... Hi Hui-Yi, I have a question about the heat map. Which value do you use to draw? Raw fluorescence intensity, normalized fluorescence intensity, or normalized log-ratio? Many thanks, Jixin ----- Original Message ----- From: "Hui-Yi Chu" To: "James W. MacDonald" Cc: bioconductor at stat.math.eth ...
written 9.9 years ago by Wang, Jixin130
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Comment: C: How to get and save normalized data from limma
... Hi Mark, Thank you so much for your kind help! I got it. Best Regards, Jixin ----- Original Message ----- From: "Mark Cowley" To: "Jixin Wang" Cc: bioconductor at stat.math.ethz.ch Sent: Wednesday, September 10, 2008 11:39:16 PM GMT -06:00 US/Canada Central Subject: Re: [BioC] How to get and ...
written 9.9 years ago by Wang, Jixin130
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Answer: A: How to get and save normalized data from limma
... Hi Mark, Thank you very much for your kind reply. I want to get normalized cy3 and cy5 channel data and tend to look at the correlation (scatter plot) of normalized data between biological replicates and dye swaps. But I can?t figure out R code for this task. I will use MeV(TM4) and Cluster/TreeVie ...
written 9.9 years ago by Wang, Jixin130
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How to get and save normalized data from limma
... Dear All, I want to use the normalized signal intensities data to do hierarchical clustering. But I don?t know how to save the normalized data from LIMMA. Below is the code: library(limma) setwd("C:/Documents and Settings/JWang/Desktop/analysis with R/RAO") targets <- readTargets("equi.txt") ...
clustering limma written 9.9 years ago by Wang, Jixin130
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Comment: C: missing value
... Hi Gordon, Got it! Thanks a lot for the email. Best regards, Jixin ----- Original Message ----- From: "Jixin Wang" To: "Jenny Drnevich" Cc: "James W. MacDonald" , bioconductor at stat.math.ethz.ch Sent: Tuesday, August 12, 2008 4:42:42 PM GMT -06:00 US/Canada Central Subject: Re: [BioC] How t ...
written 10.0 years ago by Wang, Jixin130
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Comment: C: missing value
... Hi Jenny and Jim, Thanks for the help. I have another question. In the output result of topTable, column labeled logFC is the log base 2 of fold change value instead of e. I want to make sure that. Many thanks, Jixin ----- Original Message ----- From: "Jenny Drnevich" To: "James W. MacDonald" ...
written 10.0 years ago by Wang, Jixin130
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Comment: C: missing value
... Hi Jenny, Thank you so much for your quick reply and kind help! I really appreciate it. Best regards, Jixin ----- Original Message ----- From: "Jenny Drnevich" To: "Jixin Wang" , bioconductor at stat.math.ethz.ch Sent: Tuesday, August 12, 2008 2:24:22 PM GMT -06:00 US/Canada Central Subject: ...
written 10.0 years ago by Wang, Jixin130

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