User: Seymoo

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Seymoo0
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Posts by Seymoo

<prev • 31 results • page 1 of 4 • next >
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Comment: C: Install a custom CDF file
... Great! I downloaded the annotation and converted it to a data frame `z <-z @dataTable@table`. I did follow your steps and excluded rows in **z** without available **EntrezGeneID**. But now **dim(z)=41090** and `table(isUnique(z$EntrezGeneID))`shows **29109** non unique values. this is not usual ...
written 3 months ago by Seymoo0
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Comment: C: Install a custom CDF file
... Thanks a lot James! I did try your solution but I just replaced `**ReadAffy**` with `**affy::justRMA**` and used `**cdfname = "hursta2a520709cdf, normalize = TRUE"**` and now it seems that I have a log2 transformed expression matrix.However, I am not sure if the rows (**n=60607**) are converted to ...
written 3 months ago by Seymoo0
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Install a custom CDF file
... I would like to access gene level expression data from **GSE131418** study. However, since it is not possbile to do that with "GEOquery" for some reason, I want to use the CDF file "**GPL15048_HuRSTA_2a520709.CDF.gz**" provided under "**GSE131418_RAW.tar**" to perform RMA normalization and probe s ...
annotation biobase geoquery rma makecdf written 3 months ago by Seymoo0 • updated 3 months ago by James W. MacDonald51k
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NMF pre-processsing effect on classification
... I have noticed that when I apply NMF to log2 transformed gene expression data for classification purpose the result are different than if I first do an exponential transformation of the same data matrix. Also, test statistics increase after exponential transformation. I know that NMF is not applica ...
classification bioconductor log2 nmf written 16 months ago by Seymoo0
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intra-cluster silhouette width
... I am wondering how to make a silhouette plot on the results from Mclust packge, where measure of silhouette for each sample in each group is shown? Using "Fcp" package I can check the average silhouette. mb = Mclust(iris[,-5], 3) cs = cluster.stats(dist(iris[1:4]), mb$classification) #instal ...
mclust silhouette fcp written 19 months ago by Seymoo0
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Comment: C: limma contrast matrix
... Hi @Aaron Lun . I didnt want to post a new question because I am actually a bit confused with the reversing that you just mentioned above ( e.g., N50_C - N50_D instead of N50_D - N50_C ), because by doing so this can swap the number of detected DE. I am wondering if what is generally accepted when I ...
written 19 months ago by Seymoo0
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Comment: C: convert Gene collection to gene list for camera function
... Thanks James! ...
written 20 months ago by Seymoo0
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convert Gene collection to gene list for camera function
... I want to use `camera` function in limma. I downloaded xml file from MSigDB and loaded it but I am wondering how can I make it to a compatible list for camera function as it has been mentioned in here that GEneCollection need to be converted to a list. what I have done is gsc <- getBroadSets(" ...
limma gseabase written 20 months ago by Seymoo0 • updated 20 months ago by James W. MacDonald51k
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GSA for comparison of geneset enricment analysis between multiple class
... I have a gene expression data `AllExp` and a data.frame `info` with sample name of `AllExp` as row names and first column in it specifies groups that each sample belongs to. I am trying to perform a a gene set enrichment analysis using GSA package. but I get following error `Error in cut.default(s ...
gsa written 20 months ago by Seymoo0
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Answer: A: Changing SVM-Kernal in geNetClassifier function
... @saibar Hi Sara, Thanks for making this great package. I am wondering if you add cost argument in the formula to be set by users or if you could explain how to modify it the way it is right now ? I am using Caret package to find optimal cost to be used in the function and I would like to adjust co ...
written 22 months ago by Seymoo0

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