User: Joe Kherery

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Joe Kherery100
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Posts by Joe Kherery

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Comment: C: R: Collapsed to unique genes (Affymetrix microarray)
... Hello Kevin, I try it, but dont work. ...
written 10 months ago by Joe Kherery100
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Comment: C: R: Collapsed to unique genes (Affymetrix microarray)
... Sí, pero no mucho. I did as you said, but I still get this error. Error in rowMeans(y$exprs, na.rm = TRUE) : 'x' must be numeric I tried transform `eset_fil` into data frame but same error. I triend as.matrix.... not results ...
written 10 months ago by Joe Kherery100
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Comment: C: R: Collapsed to unique genes (Affymetrix microarray)
... I will try as you exemplified. Thanks ...
written 10 months ago by Joe Kherery100
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Comment: C: R: Collapsed to unique genes (Affymetrix microarray)
... I don't think I need to read it as `ExpressionSet`, my data.txt contains probe ID names and samples ... but I don't think i can analyze it any other way ... or is it simply read use `eset_fil<-avereps(eset,ID=eset$geneID)` and do as I usually do in `limma`? f <- factor(targets$Target, ...
written 10 months ago by Joe Kherery100
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Comment: C: R: Collapsed to unique genes (Affymetrix microarray)
... Could I not do it that way? 1.Find my list of differentially expressed probes after merge with the annotation and then do the `avereps`? and remove the NA? ...
written 10 months ago by Joe Kherery100
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Comment: C: R: Collapsed to unique genes (Affymetrix microarray)
... Actually I have a data.txt file which is normalized microarray data and I also have Annotation data. I can easily analyze normalized data.txt, but in the end when i merge with my Annotation list, I end up with duplicate genes. So I decided to merge data.txt + annotations and use the `avereps` funct ...
written 10 months ago by Joe Kherery100
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Comment: C: R: Collapsed to unique genes (Affymetrix microarray)
... Hello kevin you know how to access `avereps` using the function `eset <- readExpressionSet("data.txt", header=T)` `eset_fil<-avereps(eset,ID=eset$geneID)` I always get the error: > Error in avereps.default(eset, ID = eset$geneID) : No probe IDs ...
written 10 months ago by Joe Kherery100
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Comment: C: R: Collapsed to unique genes (Affymetrix microarray)
... Thank you so much Kevin! ...
written 10 months ago by Joe Kherery100
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Comment: C: R: Collapsed to unique genes (Affymetrix microarray)
... Hello kevin I tried `avereps()` function, after compute statistics for the data, however I don't think `avereps()` did the media, it seems that he just removed the gene with the lowest value. or should I do this before generating my list of DEGs? ...
written 10 months ago by Joe Kherery100
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R: Collapsed to unique genes (Affymetrix microarray)
... I have a list of genes from an Affymetrix microarray analysis. However I have duplicate genes, I wonder how do I collapsed to unique genes by calculating the mean expression of transcripts from the same gene locus? Any information is valid. Thank you! ...
R microarray affymetrix written 10 months ago by Joe Kherery100

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