User: Rhonda DeCook

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Posts by Rhonda DeCook

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Answer: A: How to analysis the this kind of data set?
... Hi Xiao, It seems in a design such as this with Treatment and Time, there are a lot of ways to define 'differential expression'. You say you're looking for differentially expressed genes with respect to treatment(a,b,ab). So, does this mean you're not interested in any time effects(or any Treatme ...
written 14.5 years ago by Rhonda DeCook90
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Answer: A: loged data or not loged previous to use normalize.quantile
... With respect to permutations tests... I'm under the impression that you only need independence, not the assumption of constant variance. The permutation test provides us with a distribution of the test statistic under the null hypothesis (equal means in the 2-sample scenario, i.e. all data was gen ...
written 14.5 years ago by Rhonda DeCook90
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Convert (altcdfenvs)CdfEnvAffy object to useable cdf package
... Ken, I successfully created a new CDF environment for the ATH1 chip awhile ago using the altcdfenv package. I'll show you some of the code that worked for me... ## I built my new cdf environment (using a function similar to buildCdfEnv.matchprobes). > alt.cdf.all<-buildCdfEnv.pmids(pm.i.al ...
cdf probe affy convert written 14.6 years ago by Rhonda DeCook90
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selecting probe set from expression matrix
... srini, It seems like there's a lot of ways to pull-out information for a specific gene depending on the type of object you're working with. The vignettes should help you here. Once you're working with a matrix like 'ex.data', a not so elegant way is by getting the probeset names with... > dimn ...
written 14.6 years ago by Rhonda DeCook90 • updated 14.6 years ago by James W. MacDonald51k
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annotation for ath1121501 (?)
... Recent posts have made me aware of the 'geneplotter' package. This is exactly what I've been wanting to do, but for the ath1121501 chip (Arabidopsis) which does not have an annotation package available at the metadata page yet. Past posts suggest folks are working on getting the annotation for thi ...
annotation ath1121501 written 14.7 years ago by Rhonda DeCook90 • updated 14.7 years ago by Pita120
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Answer: A: Question about ATH1 array
... Fangxin, I believe if you choose the option "xy.offset=0" in the 'indices2xy' function you'll get the indices you're looking for. I was off by 1 in my initial exploration and this option (which can be set to 0 or 1) corrected the disagreement. ## For example, I used this for my affybatch called ' ...
written 14.7 years ago by Rhonda DeCook90
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Answer: A: Custom CDF Files - howto ?
... Sorry Rich, I realize now that you're working with a custom CDF 'file', not with a custom CDF 'environment' which is what I was doing. Good luck, Rhonda > > I have created a custom CDF file. > > The purpose is to measure the expression of splice > variations. > > I place th ...
written 14.7 years ago by Rhonda DeCook90
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Custom CDF Files - howto ?
... Rich, Can you tell us a little more. How was your custom CDF file created? It seems like R is not recognizing the file in your directory as a CDF file. I created a custom CDF file recently for the ATH1 chip that removed known 'SFP' probe pairs using the 'altcdfenv' package and a modification of f ...
go cdf written 14.7 years ago by Rhonda DeCook90 • updated 14.7 years ago by Richard Finney180
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alt cdf env probe index config problem
... I attempted to submit this post as a non-member last week, but it never appeared on the list. I'm re-posting as a member now, hope it isn't a duplicate... I'm using the 'altcdfenv' package to create an alternative CDF environment for the "ATH1-121501" chip. We would like to re-do our analysis on ...
go cdf probe affy written 14.9 years ago by Rhonda DeCook90

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