User: giroudpaul

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giroudpaul70
Reputation:
70
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Trusted
Location:
European Union
Last seen:
1 day, 14 hours ago
Joined:
4 years, 1 month ago
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g*********@gmail.com

Posts by giroudpaul

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Annotations for Affymetrix HT HG-U133+ PM Array Plate
... Thank you for your answer, I see you indicated me the AffyGenePDInfo, and I was not finding anything because I search for the ChipDB package, which does not exist. I did not manage to annotate my data using it though, I tried with affycoretools::annotateEset, but I get the following error : "There ...
written 6 days ago by giroudpaul70
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Annotations for Affymetrix HT HG-U133+ PM Array Plate
... Hi, I am trying to analyze a GSE that was performed on affymetrix HT HG-U133+ PM Array Plate [GPL13158][1] But I cannot find the corresponding annotation package on bioconductor. Affymetrix website is of no use, return a 404 error when selecting the array. If anyone has experience with this arra ...
affimetrix R written 7 days ago by giroudpaul70 • updated 7 days ago by Kevin Blighe52k
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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 2.7 years ago by giroudpaul70
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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 2.7 years ago by giroudpaul70
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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 2.7 years ago by giroudpaul70 • updated 2.7 years ago by Joe15k
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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 3.6 years ago by giroudpaul70
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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 3.6 years ago by giroudpaul70 • updated 3.6 years ago by igor8.9k
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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 3.7 years ago by giroudpaul70
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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 3.7 years ago by giroudpaul70
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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 3.7 years ago by giroudpaul70

Latest awards to giroudpaul

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Analyse of HGU133 set microarrays / Merge ExpressionSets
Popular Question 2.4 years ago, created a question with more than 1,000 views. For R microarray analysis : Trouble with an exercise
Popular Question 2.4 years ago, created a question with more than 1,000 views. For [Resolved] Local alternative to galaxy "Extract Genomic DNA using coordinates" tool
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Preparing a .bed for Homer annotation
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Getting Raw illumina microarray data from GEO
Popular Question 2.4 years ago, created a question with more than 1,000 views. For [Resolved] Extract Top score peaks from a .bed
Popular Question 2.4 years ago, created a question with more than 1,000 views. For [Resolved] Adding a unique ID column to a bed file
Scholar 4.1 years ago, created an answer that has been accepted. For A: Extract Top score peaks from a .bed

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