User: arronar

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arronar100
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Austria
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4 days, 8 hours ago
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3 years, 7 months ago
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Posts by arronar

<prev • 104 results • page 1 of 11 • next >
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Comment: C: nsFilter() almost always return the same number of filtered genes in different m
... Thank you very much for your answer. Do you think that the following approach is better ? library(genefilter) f1 <- pOverA(0.25, log2(100)) f2 <- function(x) (IQR(x) > 0.5) ff <- filterfun(f1, f2) selected <- genefilter(eset, ff) sum(selected) esetSub < ...
written 15 days ago by arronar100
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Non matched HG-U219 microarray probe sets.
... Hello. I'm currently trying to convert the probsets into symbols and entrez ids of a HG_U219 microarray by using the following commands Symbols = unlist(mget(probes, hgu219SYMBOL, ifnotfound=NA)) Entrez_IDs = unlist(mget(probes, hgu219ENTREZID, ifnotfound=NA)) As you know, some of the pr ...
annotation probesets microarray written 16 days ago by arronar100 • updated 15 days ago by Kevin Blighe11k
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nsFilter() almost always return the same number of filtered genes in different microarrays
... Hello. I'm about to process around 6 different microarray datasets and currently I'm working on the filtering step by using the `nsFilter()` function from `geneFilter` library. After running the raw data through the RMA algorithm, I'm using the following code with a custom function in order to re ...
R nsfilter microarray gene-filtering written 18 days ago by arronar100 • updated 17 days ago by Kevin Blighe11k
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Generating descriptors at pathway level for further use to classification methods.
... Hello. I'm having 6 different microrray experiments for 6 different drugs that treat the same disease. What I want to do now is to create some descriptors for each of these datasets at the pathway level. As far as I read the literature, I decided to use the pathifier algorithm described in [this ...
descriptors pathway classification microarrays written 28 days ago by arronar100
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Gene set / pathway analysis from a systems biology preview (?)
... Hello. On my way to read and run a pathway/gene set analysis on some microarray data, I realized that besides the fact that there are many different ways (statistical methods) to do the analysis, all of them (at least as far as I know) stays at statistic and as you already know returns a p-value or ...
systems biology pathway analysis written 4 weeks ago by arronar100
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Comment: C: What people do with the probes that doesn't have any GENE SYMBOL in annotation d
... Those probe sets that didn't map in gene symbols, were about 12000 . So I needed a more automatic way to retrieve a gene symbol for them and not one by one . So I found this [site][1] in which you configure the input as Affyid and the output as gene symbol. Then, I wrote these lines in R to retrieve ...
written 8 weeks ago by arronar100
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Comment: C: What people do with the probes that doesn't have any GENE SYMBOL in annotation d
... It would be helpful enough if you could explain the procedure with more details because I'm not so experienced with such tasks. Thank you very much. ...
written 8 weeks ago by arronar100
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Comment: C: What people do with the probes that doesn't have any GENE SYMBOL in annotation d
... I'm already using the lateset version of that package. > Package hgu133plus2.db version 3.2.3 ...
written 8 weeks ago by arronar100
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What people do with the probes that doesn't have any GENE SYMBOL in annotation databases?
... Hello. I'm doing some microarray analysis, and I figured out that some probe ids have not any GENE SYMBOL. Am I suppose to delete those probes or let them exist ? The way I apply annotation info for an Affymetrix HGU133plus2 array after RMA application, is the following: probes=row.names(expr ...
microoarrays annotation written 8 weeks ago by arronar100 • updated 8 weeks ago by Maxime Lamontagne1.9k
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Comment: C: Qs on merging microarray datasets and different ways on building a classifier on
... First of all thank you for your answer. I've already read that article and I really liked it. It's very informative and is the article that gave me to understand that there is not only the way of finding DEGs and then run classifier on them but you can just use the whole dataset. The difference now ...
written 9 weeks ago by arronar100

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