User: Brawni

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Brawni90
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90
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France
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4 years, 11 months ago
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Posts by Brawni

<prev • 24 results • page 1 of 3 • next >
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Comment: C: mismatch sample number TCGA ovary cancer between recount and GDC portal
... Hi Kevin, I have been hovering around these data in the last months and yes I understand patience is a necessary requirement, which i dont have much. I looked also at this webtool https://bioinformatics.mdanderson.org/tcgambatch/ for investigating batch effects, generated by the MD Anderson Cancer C ...
written 4 weeks ago by Brawni90
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Comment: C: mismatch sample number TCGA ovary cancer between recount and GDC portal
... Yes it's reasonable to have discrepancies, unfortunately I'm interested in acquiring normal samples from ovary and other TCGA studies, but ultimately use also the tumoral data so GTEx for example would not be a solution. I guess i will have to go for the cumbersome option. In any case does 'Legacy' ...
written 4 weeks ago by Brawni90
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Comment: A: mismatch sample number TCGA ovary cancer between recount and GDC portal
... I used recount2 cause they have put togheter many RNA-seq studies using same pipeline which is good if you want to compare studies (taking acount of possible batch effects) but actually given that i'm going to compare studies within TCGA project I may as well get them from the GDC portal, couldnt I? ...
written 4 weeks ago by Brawni90
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Comment: C: mismatch sample number TCGA ovary cancer between recount and GDC portal
... Sorry, the samples on GDC should be actually 379 belonging to TCGA-OV and 1 to TCGA-SARC. Ah! That may explain things.. I downloaded the full TCGA project cause I didnt find how to specify a single study within project with the recount package: download_study(project ='TCGA', type = "rse-gene", outd ...
written 4 weeks ago by Brawni90
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mismatch sample number TCGA ovary cancer between recount and GDC portal
... Hello there! I have been trying to understand what's going on with the RNA-seq TCGA ovary dataset as i got a different number of samples by using the recount R package and the GDC web portal. To be more specific, i get 430 tumoral samples using recount (so, no normal samples), and 379 samples from ...
tcga recount gdc ovary written 4 weeks ago by Brawni90
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Answer: A: TCGA - finding Normal and Tumor samples for matching protein and rna-seq samples
... Hey, did you check the CPTAC data? It's a consortium which have been profiling proteome and phosphoproteome of TCGA ovarian breast and colonrectal cancers, and they are continuing to do so for further TCGA studies. Here is the link for the colon-rectal study: https://cptac-data-portal.georgetown.edu ...
written 4 weeks ago by Brawni90
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Where are tissue-specific molecular pathway databases?
... Hello there, Very simple question. Is there any web-resource/database which provides tissue-specific molecular pathway maps? I have looked for databases of tissue-specific pathways with no success, but i may not be too good in searching, or how do we explain this oddity? Thanks in advance for y ...
pathway maps tissue-specific written 12 months ago by Brawni90
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Answer: A: Expression of genes in module very different to representative eigenmodule expre
... Hi there, i realise this post is 3 yrs old. Nonetheless I feel your pain and i can't help trying to help on your ancient problem. Here it is: try using the argument networkType='signed hybrid' within the function blockwiseModules. I encountered the same problem without using it as aparently even in ...
written 13 months ago by Brawni90
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Comment: C: WGCNA modules and categorical traits relationship
... Thanks a million for your answer Kevin, that is what i wanted to know. I'll try both methods you suggested! I already separated my data by another factor (tissue) as this was the main source of variance, interesting point to further divide the data too, ill dig into it! Cheers! ...
written 13 months ago by Brawni90
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WGCNA modules and categorical traits relationship
... Hi there, I have looked a bit around for this question but i haven't managed to fully understand the answers. I have done a WGCNA analysis on my data which ended up identifying several modules of co-expressed genes. Now, I would like to calculate significance of the correlation between the eigengen ...
wgcna written 13 months ago by Brawni90 • updated 13 months ago by Kevin Blighe37k

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Popular Question 10 months ago, created a question with more than 1,000 views. For Searching homologues proteins in human STRING and Blast
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