User: giroudpaul

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giroudpaul40
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40
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Location:
France
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1 year ago
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3 years, 8 months ago
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Posts by giroudpaul

<prev • 38 results • page 3 of 4 • next >
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How to : Preprocessing of Gene ST array with Oligo
... Dear Bioconductor member, I am quite a self-learning debutant with microarray analysis, but I managed to perform simple Quality Control, Preprocessing and DE analysis using affy and limma packages But now, I am starting to work with Gene ST array and I will soon have to work with Raw data from HTA ...
oligo hugene20st written 3.5 years ago by giroudpaul40 • updated 3.5 years ago by James W. MacDonald52k
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Comment: C: TopTable Problem : Unique Adj.P.Val which is near 1
... OK, I think I get it. Maybe if I filter out genes (like probes without entrez ID) I will get something significant. I may also remove low expression genes. I won't be able to reproduce the code though, since they used affymetrix softwares. But I don't intend to either, if I can get a list of DE gen ...
written 3.5 years ago by giroudpaul40
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Comment: C: TopTable Problem : Unique Adj.P.Val which is near 1
... Hum, I am pretty sure there is a problem, since : The data were published and they do find DE genes It's not just stretches, here I get adj.P.val = 0.999899 for coef=1 for all the 53617 probes I get similar value for all contrasts Any idea why that might happen ? ...
written 3.5 years ago by giroudpaul40
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TopTable Problem : Unique Adj.P.Val which is near 1
... Hi I am trying to get the DE genes from a GEO dataset (my fourth one) I began the analysis like I did for the three other datasets, for which I had no problems. But for this one, I can't see what I did differently that make it so that the TopTable give only one adj.P.Val, the same for every probes ...
limma toptable written 3.5 years ago by giroudpaul40
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Comment: C: Modifying eset@assayData$exprs : Error : cannot change value of locked binding f
... As I said, it is an illumina array dataset, boxplot shows that the normalization has already been done. The trouble is if I want to identify DE genes based on my contrasts, I need to use lmFit and eBayes from limma. It's true that I could work my way around doing lmFit(log2(exprs(eset))) (Since I ...
written 3.6 years ago by giroudpaul40
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Modifying eset@assayData$exprs : Error : cannot change value of locked binding for 'exprs'
... Hi I retrieved an expression set (Illumina HumanHT-12 V3.0) using GEOquery, but I noticed that the expr value where not in log2... So I tried to do it myself but got an error and since I am no R expert, I don't know much about environment, so I don't know how to solve this. Any idea ? Thanks ! Co ...
geoquery written 3.6 years ago by giroudpaul40 • updated 3.6 years ago by Steve Lianoglou12k
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Comment: C: Heatmap of a subset of genes
... Yes, the devel version (0.22 or higher) is way better than the Bioconductor one (0.20) However, I had a hard time installing it on windows... (Need to install Rtools first) ...
written 3.6 years ago by giroudpaul40
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Comment: C: Heatmap of a subset of genes
... Yeah, thanks, so I did extracted the exprs(data.rma)corresponding to the gene I identified with Limma. I tried heatmap, heatmap.2 and aheatmap, and I also find aheatmap is the easiest and looks betters than the other two. Two questions though. Should I Scale the data if I just take upregulated gen ...
written 3.6 years ago by giroudpaul40
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Comment: C: Heatmap of a subset of genes
... So correct me if I'm wrong: data.rma <- rma(data) data.fit = lmFit(data.rma,design) data.fit.eb <- eBayes(data.fit) And using topTable, I extract expression values for M1 and M2, and then do the subset, and that's it ? However, If I do this, I get Expression values, is it ok to plot this o ...
written 3.6 years ago by giroudpaul40
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Heatmap of a subset of genes
... Hi. I am trying to reproduce this kind of figure (Chemokines differentially regulated in the five differents cells type on top) : I would like to do the same, first with just M1 and M2 conditions, and eventually more. I would also like to be able to choose the genes in this heatmap (if you have ...
heatmap written 3.6 years ago by giroudpaul40 • updated 3.0 years ago by caroline0

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 2.5 years ago, voted at least 25 times.

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