User: giroudpaul

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giroudpaul50
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Posts by giroudpaul

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Computer specs for analysis of transcritpional datasets from litterature
... Human data only, and not based in UK, but thanks for the offer :) Yeah I read about the cloud computing solution, but as for the possible university cluster, I first need to learn how to use this kind of solution, as I've only worked locally for now. ...
written 8 months ago by giroudpaul50
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Comment: C: Computer specs for analysis of transcritpional datasets from litterature
... Thank you both for your answer ! I do have an affiliation with a research institute linked with an hospital, but the access to a bioinformatic server from outside the institute still have to be discussed. You confirm my fear that most public accessible data are raw data. I used galaxy before with ...
written 8 months ago by giroudpaul50
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Computer specs for analysis of transcritpional datasets from litterature
... Hi Biostar Community, I'm starting my PhD in a small company and my subject will require to mine data from literature transcriptional analysis (microarray/RNA-seq). I might also have to analyses a couple RNA-seq experiment myself. I already analyzed microarray data, and I know you don't need a bea ...
hardware written 8 months ago by giroudpaul50 • updated 8 months ago by jrj.healey3.0k
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Comment: C: Getting Raw illumina microarray data from GEO
... So how I am supposed to deal with the data available ? Perform QC and see if it's already ok and then proceed with limma DE analysis seems reasonable ? ...
written 19 months ago by giroudpaul50
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Getting Raw illumina microarray data from GEO
... Hi I want to analyze some publicly available Dataset one GEO, that uses the IlluminaHuman12 v4 beadarray (such as GSE49240) Using `gse <- getGEO("GSE49240")`, it downloaded `GSE49240_series_matrix.txt.gz`. However, I understood from GEOquery vignette that the RAW data should be accessed with ` ...
geo illumina geoquery microarray getgeo written 19 months ago by giroudpaul50 • updated 19 months ago by igor4.9k
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Comment: C: trouble in blasting the seq file
... I don't know Blast2Go specifically, but maybe reducing the number of sequences you provide as it seems to be the problem (for example 8 times 10000 sequences instead of 80000 at once) ? ...
written 20 months ago by giroudpaul50
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Analyse of HGU133 set microarrays / Merge ExpressionSets
... Hello, I am currently trying to extract data from a GEO dataset which has been done on the Affymetrix HGU133 plateforme, meaning that all samples were done on two different chip : hgu133a and hgu133b. Applying the advises presented here : https://support.bioconductor.org/p/5339/#5341 https://sup ...
R hgu133 bioconductor expressionset microarray written 20 months ago by giroudpaul50
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Comment: C: R microarray analysis : Trouble with an exercise
... What do you mean ? I just follow the exercise, because it was a nice step by step exercise, with quite good explanation of the code. But I can't really say if it's correct or not. Maybe you know better trainings ? ...
written 20 months ago by giroudpaul50
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Comment: C: R microarray analysis : Trouble with an exercise
... That was it ! Ok, I really need to improve my R skills before going deeper in the microarray analysis ! Thank you ! Edit, actually, to have it correct with the exercises, so in order to have 50 genes, and not 49, I just need to do this : sampleNames = c(sampleNames,rep(ph@data[i,1],51)) fe ...
written 20 months ago by giroudpaul50
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R microarray analysis : Trouble with an exercise
... Hello, I'm trying to understand how to analyze microarray data with R and Bioconductor. I found this quite nice and complete course for debutant (both for R and microarray analysis) : [Link][1] However, I'm stuck with "Exercise 8 : create a heat map of normalized intensities of the first 50 genes u ...
R bioconductor ggplot microarray heatmap written 20 months ago by giroudpaul50 • updated 20 months ago by Michael Dondrup43k

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Scholar 2.1 years ago, created an answer that has been accepted. For A: Extract Top score peaks from a .bed

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