User: julin@aecom.yu.edu

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Posts by julin@aecom.yu.edu

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unbalanced block design using limma
... Dear List, I am using limma to analyze a affy ST1.0 dataset. I have 6 patients from which I have two tissue types: tumor and non- tumor. One of the sample has a technical repeat, resulting 12 arrays. I would like to compare tumor vs. non-tumor and incorporate the pairing and technical repeat ...
affy limma written 8.7 years ago by julin@aecom.yu.edu80
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Any way to ouput the reordered gene list from heatmap.2()?
... Hi dear all I am using the heatmap.2 function in the gplots package to draw a heatmap of 297 gene list. The plot looks very nice. But since the rows(genes) were reordered along with the dendrogram, is there any way to output this reordered gene list from heatmap.2()? The code I used is as below ...
written 9.3 years ago by julin@aecom.yu.edu80 • updated 9.3 years ago by Di Wu190
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Error messages from eBayes()(limma)
... Dear All, 1. I am working on a microarray dataset. The array platform is GeneChip Mouse Gene 1.0 ST Array. The experiment design is very straight forward: two groups comparison--control vs. treatment, with three chips in each group. 2. 3. Below is my code: > library(limma) > T ...
microarray written 9.4 years ago by julin@aecom.yu.edu80 • updated 9.4 years ago by James W. MacDonald50k
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Help: Problems with LmFit
... Dear List, I am working with six 27K human cDNA chips.Three of them are for Average Primary Tumor Cells and another three are for Invasive cells.In all chips, the reference in on the red channel, and the tumor samples are on the green channel. Here is my target file: ID FileName Cy3 ...
cancer limma written 10.2 years ago by julin@aecom.yu.edu80
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Limma design matrix for a complicated experiment design
... Dear list, I am writing to ask if anyone can help me to define a design matrix for our experiment. I am working with MoGene ST1.0 chips.Samples are from WT or HIV- transgenic mouse bone marrow-derived macrophages that we grew in dishes and then either exposed to TB or not for 24 hours. Each pair i ...
limma written 10.6 years ago by julin@aecom.yu.edu80
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Comment: C: problem with function rma
... Martin, It works after I change the order of phenoData names! And I will update both R and bioconductor today. Thanks a lot for your help! Juan -----Original Message----- From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: Tuesday, May 29, 2007 9:27 PM To: Juan Lin Cc: bioconductor at stat.mat ...
written 12.0 years ago by julin@aecom.yu.edu80
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problem with function rma
... Hello Bioconductorers, I am working with 12 affy rat2302 chips recently. It was OK when I tried to read my cel files into R: > RatData<-ReadAffy() > list.celfiles() [1] "Rat 16hrs-1-2113.CEL" "Rat 16hrs-2-2114.CEL" "Rat 16hrs-3-2115.CEL" [4] "Rat 30hrs-1-2116.CEL" "Rat 30hrs-2-2117. ...
normalization rat2302 cdf genefilter affy simpleaffy affyqcreport affyio written 12.0 years ago by julin@aecom.yu.edu80 • updated 12.0 years ago by Seth Falcon7.4k
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Help:How to do normalization with Ambion bioarray data?
... Dear All: Recently I did some Ambion bioarray (one color hybridization), and got data of 6 arrays in 3 gpr files(in each gpr file there will be two array which being designated as block1 and block 2)from GenePix. I am having trouble to normalize my data. Can anyone kindly give me any clue? Thanks a ...
cancer written 12.5 years ago by julin@aecom.yu.edu80 • updated 12.5 years ago by Al Ivens270

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Popular Question 8.7 years ago, created a question with more than 1,000 views. For Any way to ouput the reordered gene list from heatmap.2()?

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