User: aaragak1

gravatar for aaragak1
aaragak10
Reputation:
0
Status:
New User
Last seen:
12 hours ago
Joined:
3 months, 3 weeks ago
Email:
a*******@jhmi.edu

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by aaragak1

<prev • 9 results • page 1 of 1 • next >
0
votes
0
answers
55
views
0
answers
Comment: C: GSVA score and 1-Pearson correlation results do not harmonize
... I'm clustering using the normalized, log transformed expression of the 8 or so genes that were used to generate the GSVA score - returning to the roots of the dataset, if you will. I think you bring up a good point about not necessarily seeing two distinct clusters. I think was confused me the most ...
written 1 day ago by aaragak10
0
votes
0
answers
55
views
0
answers
Comment: C: GSVA score and 1-Pearson correlation results do not harmonize
... Histogram of enrichment scores, showing bimodality: ![Histogram of Enrichment Scores][1] Hierarchical clustering using a euclid distance metric ![Hierarchical Clustering, Euclid Distance][2] Hierarchical clustering using a 1- pearson correlation distance ![Hierarchical Clustering, Pearson Di ...
written 1 day ago by aaragak10
0
votes
0
answers
83
views
0
answers
Comment: A: Ensembl ID to ENTREZ best converter
... BioMart, as others have mentioned, tends to work pretty well. Have you removed the version numbers off the end of the ensembl ID? (ie 1234567.89 --> 1234567) ...
written 1 day ago by aaragak10
0
votes
0
answers
55
views
0
answers
GSVA score and 1-Pearson correlation results do not harmonize
... I calculated `GSVA` scores for a large set of tumors using a fairly small set of genes (~8 genes in the signature). I found there to be a distinct bimodal distribution in my data (yes, `mx.diff = T`). I then wanted to see if I could 'orthogonally' verify this by hierarchical clustering the tumors ...
R gsva clustering written 1 day ago by aaragak10
2
votes
1
answer
84
views
1
answer
Spectral Clustering for TCGA/Gene Expression Data
... Hello all, I've been using `M3C` for consensus clustering on TCGA data to get an estimate on how many 'real' clusters of tumors are in these data. I'm wondering if and when spectral clustering should be applied vs others (hc, pam, km). Thanks for your time! ...
R rna-seq written 7 weeks ago by aaragak10 • updated 7 weeks ago by Jean-Karim Heriche22k
0
votes
2
answers
113
views
2
answers
Comment: C: Inter-RNAseq dataset operations?
... Beautiful! Thank you very much! ...
written 8 weeks ago by aaragak10
0
votes
2
answers
113
views
2
answers
Comment: C: Inter-RNAseq dataset operations?
... Thank you for your answer. I don't know if this falls quite into the realm of differential gene expression as I know it, since rather than doing intradataset operations I'm doing interdataset operations. I'm curious about what steps I might need to take in order to make sure that these two dataset ...
written 8 weeks ago by aaragak10
4
votes
2
answers
113
views
2
answers
Inter-RNAseq dataset operations?
... Hello all, I have two RNAseq datasets that came from separate experiments/studies, but I'm not entirely sure where I can find the best practices on comparing/merging one with another (or if I even should). In an ideal scenario I would like to do hierarchical clustering and/or GSVA with the two data ...
rna-seq written 8 weeks ago by aaragak10 • updated 8 weeks ago by kristoffer.vittingseerup3.2k
3
votes
2
answers
148
views
2
answers
ENSG-like CATG Identifier?
... Hello all, I've been giving some expression data which has rather perplexing identifiers. Along with Ensembl ENSG identifiers, it also has similar CATG identifiers (eg CATG00000000004) that I can seem to find nothing about. I know the answer is probably obvious to the initiated, but I'm stumped - a ...
rna-seq written 3 months ago by aaragak10 • updated 12 weeks ago by Mpiro40

Latest awards to aaragak1

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1813 users visited in the last hour