User: elenichri

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elenichri10
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10
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New User
Location:
Singapore
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1 year, 1 month ago
Joined:
4 years, 3 months ago
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Posts by elenichri

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Ilumina Genome Studio: How to extract control_probe_profile?
... Thank you Andrew. I will try to find it and if not I will use the lumidat package. I was not aware of that. Best regards, Eleni ...
written 3.9 years ago by elenichri10
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Comment: C: Ilumina Genome Studio: How to extract control_probe_profile?
... Thank you Andrew. Yes, this is what I am looking for...however, when my analysis is done, I don't see this table in my options (fig 88). It does not appear at the output as well, even when I restore the view to the IGS defaults. Is this possible under any conditions or it means that I did something ...
written 3.9 years ago by elenichri10
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Ilumina Genome Studio: How to extract control_probe_profile?
... Dear Biostars community, I am analyzing a microarray gene expression dataset generated with the Illumina human ht-12 v4 platform. I have loaded the raw image data to Genome Studio and calculated the sample_probe_profile (I am interested in the probe-level measurement). I want to extract the raw dat ...
controls illumina genome studio written 3.9 years ago by elenichri10 • updated 3.9 years ago by andrew.j.skelton735.9k
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Comment: C: Limma analysis - decomposition problem
... I have the same problem with lmFit! Have you found any solution yet? I have log2 transformed data as well. Thanks a lot! ...
written 4.0 years ago by elenichri10
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Comment: C: Normalization based on housekeeping genes
... Thank you so much for these two resources Andrew. They are really informative! ...
written 4.0 years ago by elenichri10 • updated 2 days ago by RamRS25k
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Answer: A: Functional annotation for cancer meta-signature lung cancer genes.
... Hi there! Why don't you tryDavid tool for functional annotation? Or Webgestalt tool? The latter can perform GO enrichment, KEGG enrichment and many others. You just upload your set of genes. Good luck! ...
written 4.0 years ago by elenichri10 • updated 2 days ago by RamRS25k
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Normalization based on housekeeping genes
... Dear Biostars team, I have a gene expression dataset which is produced by Illumina HTv14 microarray platform. I have performed log-transformation and quantile normalization between samples based on all genes of the array. Now my  boss asked to see the absolute levels of a gene of interest, thus ask ...
R microarray normalization written 4.0 years ago by elenichri10 • updated 4.0 years ago by andrew.j.skelton735.9k
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Comment: C: limma: logFC column in topTable
... I was applying the topTable function on the same exact data, I was using exactly the same command. Maybe I accidentally did something wrong and overwritten it...I don't know how to convert it back so I see me switching to the use of toptable instead.  Anyway, thank you for your time and help!   ...
written 4.2 years ago by elenichri10
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Comment: C: limma: logFC column in topTable
... Thank you, this is understandable. My worry is though why until some time ago, using exactly the same topTable command, I could see a logFC column and now I cannot. Any clues on that? I suspect I may have overwritten the original topTable function. If this is the case, I don't know how to fix it..If ...
written 4.2 years ago by elenichri10
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Comment: C: limma: logFC column in topTable
... I want to use topTable...Yes, please, answer to me regarding topTable. I would like to know why I cannot see the logFC column there. I just mentioned that when I use toptable I can see it...in case this is somehow informative about the source of the problem. Thanks again. ...
written 4.2 years ago by elenichri10

Latest awards to elenichri

Popular Question 2.9 years ago, created a question with more than 1,000 views. For Ilumina Genome Studio: How to extract control_probe_profile?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Normalization based on housekeeping genes
Popular Question 2.9 years ago, created a question with more than 1,000 views. For limma: logFC column in topTable
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Limma Contrast matrix

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