User: giroudpaul

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giroudpaul40
Reputation:
40
Status:
New User
Location:
France
Last seen:
12 months ago
Joined:
3 years, 7 months ago
Email:
g*********@gmail.com

Posts by giroudpaul

<prev • 38 results • page 2 of 4 • next >
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Comment: C: Trouble annotating HTA microarray
... Thanks, that's nice to see such rapid support and fix ! I will look it up. ...
written 3.3 years ago by giroudpaul40
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Trouble annotating HTA microarray
... Dear bioconductor members, I finally got my hands on results of HTA 2.0 microarray experiments, and I started processing them using the standard methods. Reading CEL files, and performing RMA doesn't pose problems, for RMA I used oligo this way : > data.rma = oligo::rma(data, background=TRUE, ...
hta pd.hta.2.0 hta20sttranscriptcluster.db written 3.4 years ago by giroudpaul40 • updated 3.4 years ago by James W. MacDonald52k
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Comment: C: Annotating the Human Gene 2.0 ST Array annotate with hugene20sttranscriptcluster
... you may try the pd.hugene.2.0.st which provide all the annotations for the platform, I found it easier as a non expert. But for the explication, I will suggest you look at the reference manual of each of theses package, it tell exactly what they do. ...
written 3.4 years ago by giroudpaul40
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Comment: C: converting amino-acid one letter code into cDNA sequene
... Well it's easier to convert a DNA sequence into protein sequence. Here you will face a problem, caused by the Genetic Code redundancy (see https://en.wikipedia.org/wiki/Genetic_code#RNA_codon_table) In other words, one amino acide can be coded by different DNA codons. Thus, if you want to create ...
written 3.4 years ago by giroudpaul40
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Comment: C: TopTable Problem : Unique Adj.P.Val which is near 1
... Well I checked the PCA plot yesterday after our talk, and this confirmed tour statements that the dataset was rubbish. I didn't understood that they were using unadjusted P in the paper (though they just simplified the term, but meant the adjusted p.val). Thanks for the salvation code, sadly, the 6 ...
written 3.5 years ago by giroudpaul40
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Comment: C: TopTable Problem : Unique Adj.P.Val which is near 1
... ^^ I "know" it because I already analyzed other dataset with similar conditions, on affy hgu133 and Illumina HT 12, and found DE genes without problems. I'll have to investigate the batch effect though. Well thank you for your help, and let that be a lesson for me :) ...
written 3.5 years ago by giroudpaul40
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Comment: C: TopTable Problem : Unique Adj.P.Val which is near 1
... So I kind of have no other choice than abandon this dataset ? Is it frequent to have zero evidence of differential expression ? Because I am waiting for my own results of an HTA chip, I don't want to tell my chief that it will be unusable because of bad luck :(   ...
written 3.5 years ago by giroudpaul40
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Comment: C: TopTable Problem : Unique Adj.P.Val which is near 1
... Yes, I read the paper and no, I am not trying to reproduce, but I want to analyze their data by myself (to answer my questions which differ from theirs). I can't reproduce, since, as it is described, they performed the analysis using Affymetrix Expression Console and Transcriptome Analysis console, ...
written 3.5 years ago by giroudpaul40
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Comment: C: TopTable Problem : Unique Adj.P.Val which is near 1
... Hi, so I did myself the whole preprocessing and filtering. I have in the end 38598 probeset that are associated to a gene. Again, topTable give me, for one comparison, an adj.P.Val close to one (and always the same). Even if I remove more data by excluding gene with a low Amean (fit.con.eb <- e ...
written 3.5 years ago by giroudpaul40
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Comment: C: How to : Preprocessing of Gene ST array with Oligo
... Well, thank you, that's all clear now. I guess I got confused by the row numbers which I wasn't sure if it was IDs or not. Thank you for the tip with annotateEset, seems easier than what I was doing before. ...
written 3.5 years ago by giroudpaul40

Latest awards to giroudpaul

Popular Question 12 months ago, created a question with more than 1,000 views. For TopTable Problem : Unique Adj.P.Val which is near 1
Popular Question 12 months ago, created a question with more than 1,000 views. For Heatmap of a subset of genes
Popular Question 19 months ago, created a question with more than 1,000 views. For Meta-analysis of microarrays (and RNA-seq) data
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Heatmap of a subset of genes
Supporter 2.4 years ago, voted at least 25 times.

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