User: Hui-Yi Chu

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Hui-Yi Chu160
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Posts by Hui-Yi Chu

<prev • 16 results • page 1 of 2 • next >
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signals subtraction
... Dear list, I have one question regarding microarray data comparisons using Affymatrix yeast whole genome chips. Here are my samples: strains-- WT vs mut, each of them has Total RNA (named as T), translating mRNA (named as P), non-translating mRNA (named as NP) and goes to each chip. Therefore, the ...
microarray limma convert written 10.0 years ago by Hui-Yi Chu160
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problem in read.table
... Dear list, I got a weird problem when I tried to use read.table to import my data matrix for drawing heatmaps. I have two different txt files generated in same way. The first one worked fine when imported into R using code1(listed below), and the second one got lots of warning messages using code2 ...
written 11.0 years ago by Hui-Yi Chu160
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scale questions
... Dear List, I think this may be a simple question for you but I wanna make it sure for further steps. I have already done some of data pre-processing procedures for my affymetrix yeast2 arrays. My next step is to get *ratios* from various conditions in wt and mutant following by fold-change comparis ...
written 11.1 years ago by Hui-Yi Chu160 • updated 11.1 years ago by Sean Davis21k
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Comment: C: questions about altcdfenv
... Got it!!! It works well..Thank yo so much... I am really not good in programing.. Many thanks! Hui-Yi On Thu, Oct 2, 2008 at 5:51 PM, Jenny Drnevich wrote: > Yes, you need to sub-set your probeIDs. You can simply do this to make > sure it has the same probesets as your esetsub: > > p ...
written 11.1 years ago by Hui-Yi Chu160
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Comment: C: questions about altcdfenv
... Hi Jenny, These precious codes are really working fine for me!!!!! Also, I went though all of the analysis I knew of the new ExpressionSet and got no problem and more reasonable results even there are still have some blank gene symbols. One more question is I still have to build my own data frame ...
written 11.1 years ago by Hui-Yi Chu160
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Comment: C: questions about altcdfenv
... Thank you Mark and Jenny!! I agree with Mark, the problem is the "yeast2.db" makes me misunderstand that it is an annotation package with both S. cerevisiae. and S. pombe. This indeed explain my odd result. Not sure if you need it, but here is the S. pombe genome database. HTH. http://www.genedb.org ...
written 11.1 years ago by Hui-Yi Chu160
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Answer: A: questions about altcdfenv
... Dear BioC list, Before turning to use altcdfenv package, I used genefilter package to generate a "filtered" expressionSet, but after filtration and annotation, it still contained lots of blank gene symbols. Some of those probesets without symbols are from S.Pombe, so that is the reason going back t ...
written 11.1 years ago by Hui-Yi Chu160
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questions about altcdfenv
... Hi, I am using Affymetrix yeast2 array so that I wanna get rid of S. pombe gene expression value before further analysis. Earlier I was using filtration function to filter out the lowest signals which I assumed from S. pombe. However, this method seems not perfect since I got the result. Thus, I tu ...
go yeast2 cdf probe written 11.1 years ago by Hui-Yi Chu160 • updated 11.1 years ago by Jenny Drnevich1.9k
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Comment: C: limma2annaffy output and heatmap questions
... Hi Jixin, I believe the normalized intensity were used based on my code. Now I am trying to draw them with the value of ratio (on the basis of wt expression value). Cheers for everybody and me, Hui-Yi On Sat, Sep 27, 2008 at 11:23 PM, Wang, Jixin wrote: > Hi Hui-Yi, > > I have a ques ...
written 11.1 years ago by Hui-Yi Chu160
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Answer: A: limma2annaffy output and heatmap questions
... Hi everyone, Just wanna say that I found the reason why I got the odd result of fold change from limma2annaffy function: Since I've subsetted my eset as esetsub, the arg of limma2annaffy must be "esetsub" rather than "eset". Thank you everyone and cheers, Hui-Yi On Fri, Sep 26, 2008 at 5:02 ...
written 11.1 years ago by Hui-Yi Chu160

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