User: Claudia

gravatar for Claudia
Claudia10
Reputation:
10
Status:
New User
Location:
Sweden
Last seen:
2 years, 7 months ago
Joined:
5 years, 5 months ago
Email:
c**********@katamail.com

Posts by Claudia

<prev • 9 results • page 1 of 1 • next >
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Question on fold change calculation for microarray data
... Dear list, I'm sorry as this is probably an easy question but I would greatly appreciate some help. I'm trying to reanalyze some published microarray data. I have two conditions (fasted and sated state) and 12 samples for each condition (before and after food intake). I'm interested in what happens ...
limma logfc fold change written 2.6 years ago by Claudia10 • updated 2.6 years ago by Gordon Smyth37k
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Comment: C: Error with oligo: environmentIsLocked
... Dear James, once more, thank you so much for your time and precious help: everything works now . Claudia ...
written 3.7 years ago by Claudia10
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Error with oligo: environmentIsLocked
... Dear all. When trying to read my cel files (Affymetric Hugene 1.0 ST array) with the oligo package, if I add the phenoData I receive this error: > phenoData <- read.table("pheno.txt", sep="\t", header=TRUE) > exp.data <- read.celfiles(filenames=list.celfiles(), phenoData=phenoData) Er ...
genefilter oligo bioconductor written 3.7 years ago by Claudia10 • updated 3.7 years ago by James W. MacDonald49k
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Comment: C: "Subscript out of bounds" erorr during microarray analysis with Limma
... I will work on this, thanks you for all the suggestions. ...
written 3.8 years ago by Claudia10
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Comment: C: "Subscript out of bounds" erorr during microarray analysis with Limma
... That is correct. If I analyze the data this way I found no genes with a significant adjusted p-value, and very few nominal significant genes at all, and these results look a bit strange to me. Do you see something else that I may have done wrong or have any other suggestions on how I should run this ...
written 3.8 years ago by Claudia10
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Answer: A: "Subscript out of bounds" erorr during microarray analysis with Limma
... Thank you for your explanation. In order to test whether or not there are differentially expressed genes the two groups and the associated p-values should I use a different model? Should I do something like this or are there better ways to test my hypothesis? library(limma) design <- model.matr ...
written 3.8 years ago by Claudia10
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Answer: A: "Subscript out of bounds" erorr during microarray analysis with Limma
... Thank you a lot for your suggestion. I tried what you suggested and it worked, but the p-values I obtain seem to be exagerately low to be real. > topTable(fitE, coef=1)                  logFC  AveExpr        t            P.Value       adj.P.Val         B 8112916 14.38131 14.37817 750.9670 1.3711 ...
written 3.8 years ago by Claudia10
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"Subscript out of bounds" erorr during microarray analysis with Limma
... Hello. I'm trying to analyze some affymetrix human gene st 1.0 arrays with oligo and limma and I receive an error when I try to generate a toptable.  To keep things simple for the moment, I would just like to see differential expression on the base of the dichotomous variable Diagnosis of my pheno ...
limma oligo bioconductor affymetrix microarrays written 3.8 years ago by Claudia10
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Comment: C: getAnnMap: package hugene10stv1 not available
... Thanks a lot for the help, I will see the vignette and try to analyze my data with these packages. Claudia On Sun, Nov 3, 2013 at 11:26 PM, Vincent Carey wrote: > with bioconductor these arrays can be processed with oligo (please see the > vignette) and annotation comes from pd.* packages ...
written 5.5 years ago by Claudia10

Latest awards to Claudia

Popular Question 2.6 years ago, created a question with more than 1,000 views. For Error with oligo: environmentIsLocked
Popular Question 3.7 years ago, created a question with more than 1,000 views. For "Subscript out of bounds" erorr during microarray analysis with Limma

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