User: Giusy Della Gatta

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Posts by Giusy Della Gatta

<prev • 11 results • page 1 of 2 • next >
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Answer: A: two color arrays normalization
... Hi Jenny, I modified again the script, but I am still stuck with this analysis. I am interested into have as output the M values of all my microarray (3 control and 3 treatment). We will manually calculate the differentially expressed genes and the most significative ones. I followed your advices, ...
written 8.8 years ago by Giusy Della Gatta110
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Answer: A: two color arrays normalization
... Thank you Jenny! Not only the controls but all the arrays are going all the way round! With yours advices the values are (correctly) switched: > fit$coef[1:5,] ctrl treat [1,] -0.024321790 0.03127735 [2,] -0.022173037 0.04670783 [3,] -0.007570963 0.05101542 [4,] -0.144515478 ...
written 8.8 years ago by Giusy Della Gatta110
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Answer: A: two color arrays normalization
... Hi Naomi, I don't know if I understood correct. I switched the signs of the design and the contrast matrices, but I still have the same results: controls going at the opposite way. > library(limma) > # Read in data files > targets=readTargets("target_frame_ltbarc_pgedit.giusy") > RG< ...
written 8.8 years ago by Giusy Della Gatta110
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Answer: A: two color arrays normalization
... Hi Naomi, I performed the analysis of my micorarrays,but still I don't manage to revert the channels! My experiment consisted into infect cells with an adenovirus: an emty one and an adenovirus expressing for a specific protein. Then I treated the same cells with a specific drug or simply with the ...
written 8.8 years ago by Giusy Della Gatta110
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Answer: A: two color arrays normalization
... Hi Naomi, I studied the model matrix command and it seems that is the one that I need to construct a new matrix and specify which will be my reference. >From LIMMA user's guide is not clear when I have to use this command. In the guide I found this example: It is a two-color microarray experime ...
written 8.8 years ago by Giusy Della Gatta110
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two color arrays normalization
... Hi everybody, I am analyzing two color Agilent microarrays by using LIMMA package. In my specific case the red channel is representing "the reference" while the green channel is "the treatment". Is it enough to use the Target File composition to specify the name of the samples and their corrispond ...
limma written 8.8 years ago by Giusy Della Gatta110 • updated 8.7 years ago by Jenny Drnevich1.9k
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bioconductor for beginners
... Hi everybody! I am a biologist and also a beginner in the use of Bioconductor and in general of the bionformatic tools for the management, analysis and interpretation f microarray data. I was wondering if someone of you can suggest me some workshop to attend, so that I can correctly learn the use ...
written 8.8 years ago by Giusy Della Gatta110 • updated 8.8 years ago by Paolo Sonego140
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Answer: A: read.maimages in limma package
... Thank you Peter, I'll check it out! I have also seen that I have to make a file in which I have to describe agilent annotations (see point 3 of my previuos email). May you know where I have to check to retrieve informations on the file format that I have to use? Thank you G -----Original Messag ...
written 8.9 years ago by Giusy Della Gatta110
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read.maimages in limma package
... Hi! I am analyzing custom two color agilent array by using limma package and I am having some problems with the read.maimages comand: I launch this comand: > read.maimages("Targets$Filename, source="agilent") and the error that I have is the following: Read Control_2b.txt Read Control_3b.txt ...
limma written 8.9 years ago by Giusy Della Gatta110
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Answer: A: targets frame
... Thank you Kasper, I uploaded the file and I was trying to make the RG list but I got this message: > library (limma) > targets <- readTargets("target_frame_barc.txt") > RG <-read.maimages (targets$FileName, source="agilent") Error in read.maimages(targets$FileName, source = "agilent ...
written 8.9 years ago by Giusy Della Gatta110

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