User: Erika Melissari

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Posts by Erika Melissari

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array/spot quality control procedure on gene expression microarrays: What weights?
... Dear all, I am starting a statistical analysis for a new experiment and I have some doubts about quality control filtering procedure. I know quality control is essential in order to obtain a "reliable" result at the end of statistical analysis. Usually I discard spots by setting a convenient wt.fun ...
normalization assign written 10.8 years ago by Erika Melissari240
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Answer: A: agi4x44kpreprocess package
... Re: [BioC] agi4x44kpreprocess packageThank you for your information. Actually, this charateristic do not result clearly from the vignette. It's a pity that this package is not for two-color analysis: it is very nice! Thank you Erika ----- Original Message ----- From: Pedro López Romero To: ...
written 10.8 years ago by Erika Melissari240
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Answer: A: agi4x44kpreprocess package
... Hello Sean, then perhaps does agi4x44preprocess package analyze only Agilent one- color microarray? Vignette of this package (http://www.bioconductor.org/packages/2.3/bio c/vignettes/Agi4x44PreProcess/inst/doc/Agi4x44PreProcess.pdf) indicates a template of targets like this: > targets ...
written 10.8 years ago by Erika Melissari240
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Answer: A: agi4x44kpreprocess package
... Hello Francois, thank you for your help. here is the sessionInfo() output R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attache ...
written 10.8 years ago by Erika Melissari240
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agi4x44kpreprocess package
... Hello all, does anyone know Agi4x44kPreProcess package? I'm exploring it to perform pre-process steps on human 4x44k Agilent microarrays, but I have a question or perhaps a doubt: why does this package load only the green signals (processed, mean, ect.) and not the red signals? Is it an error of th ...
written 10.8 years ago by Erika Melissari240 • updated 10.8 years ago by Pedro López Romero360
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Answer: A: Use of duplicateCorrelation
... Dear Gordon, I fixed the problem with eBayes....I used ebayes() and not eBayes() and, as reported in LIMMA help, "ebayes is the earlier and leaner function. eBayes is intended to have a more object-orientated flavor as it produces objects containing all the necessary components for downstream analy ...
written 10.8 years ago by Erika Melissari240
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Use of duplicateCorrelation
... Hello all, I'm studing how to use duplicateCorrelation() of LIMMA package in order to evaluate the between-arrays correlation. I have a simple experiment of direct comparison with dye-swap as follows: targets SlideNumber FileName Cy3 Cy5 Date 1 A ...
limma written 10.8 years ago by Erika Melissari240
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Answer: A: Removing control probes before fitting the linear model
... Hello, I found out that in some examples (11.5 and 11.6) of Limma userguide it is suggested the removal of the control probes from the data before fitting the linear model. Usually I flag negative or positive control spots as "not good" by using a wt.fun function during the loading of the data (e.g ...
written 11.1 years ago by Erika Melissari240
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Removing control probes before fitting the linear model
... Hello, I found out that in some examples (11.5 and 11.6) of Limma userguide it is suggested the removal of the control probes from the data before fitting the linear model. Usually I flag negative or positive control spots as "not good" by using a wt.fun function during the loading of the data (e.g ...
limma written 11.1 years ago by Erika Melissari240 • updated 11.1 years ago by Gordon Smyth39k
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Balanced Block design in LIMMA
... Hello all, I am planning the experimental design for a new microarray experiment. We are interested in studying the effect of a new drug on treated mice respect to untreated mice. In order to obtain an efficient experiment, we would like to use a balanced block design, that is to balance the sample ...
microarray limma written 11.1 years ago by Erika Melissari240 • updated 11.1 years ago by Gordon Smyth39k

Latest awards to Erika Melissari

Popular Question 10.2 years ago, created a question with more than 1,000 views. For Use of duplicateCorrelation
Popular Question 10.2 years ago, created a question with more than 1,000 views. For avereps function

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