User: atakanekiz

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atakanekiz20
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Posts by atakanekiz

<prev • 25 results • page 1 of 3 • next >
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Comment: C: BioMart does not find mouse homologs of human genes
... Wow, interesting! You are right, it looks like Ensembl and NCBI don't agree on this. I will side with NCBI in this case. Do you have a recommendation on how to find orthologs in an all-inclusive manner? I thought Ensembl was the most comprehensive one, but I may be wrong based on this experience. ...
written 8 days ago by atakanekiz20
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Comment: C: BioMart does not find mouse homologs of human genes
... Thanks for the answer. I thought something may be going wrong in the `biomaRt` rather than the actual database. I'll keep digging to see what's up. ...
written 9 days ago by atakanekiz20
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Comment: C: BioMart does not find mouse homologs of human genes
... We work on this gene in both human and mouse models. Below is the mouse entry in ensembl: http://uswest.ensembl.org/Mus_musculus/Gene/Summary?g=ENSMUSG00000097418;r=16:84703167-84715245 ...
written 9 days ago by atakanekiz20
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BioMart does not find mouse homologs of human genes
... Hello BC community, I am trying to convert a list of human genes to mouse homologs using R. Biomart finds homologs of some genes but not others. I can't seem to figure out the reason for this behavior. An example code is below. human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") ...
biomart ensembl homolog ortholog gene conversion written 10 days ago by atakanekiz20 • updated 10 days ago by James W. MacDonald51k
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Comment: C: Unexpected results while analyzing a subset of genes in GEO RNAseq dataset conta
... Thanks for the insights! ...
written 15 days ago by atakanekiz20
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Comment: C: Unexpected results while analyzing a subset of genes in GEO RNAseq dataset conta
... It makes sense, thanks! Just out of curiosity... When I skip the `contrasts.fit` step what is actually being calculated giving the same output when I call the `topTable` function? Since the reported "upregulated" genes are always the highly expressed ones, it feels like the genes are compared agai ...
written 16 days ago by atakanekiz20
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Comment: C: Unexpected results while analyzing a subset of genes in GEO RNAseq dataset conta
... @Gordon, thanks so much for the input. I read that thread prior to my analysis but I will go back, and read it again with a fresh pair of eyes. I'd appreciate your insights on the follow-up questions I added in the comments. Best, Atakan ...
written 17 days ago by atakanekiz20
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Comment: C: Unexpected results while analyzing a subset of genes in GEO RNAseq dataset conta
... Thanks for the insights! I got it to work now and it makes sense. I'd appreciate if you can help me understand two couple more points about this analysis (see below) ### First to comment on your points: 1) The data contained transcript IDs which may correlate with different isoforms of the same ho ...
written 17 days ago by atakanekiz20
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Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
... Hello BioC community, Let me set the stage for my question first. We generated a list of 200 genes that correlate with certain clinical parameters using human RNAseq data. I'd like to analyze the expression patterns of these genes in published GEO datasets. One of the GEO datasets I'm interested in ...
rnaseq limma R differential expression tpm written 17 days ago by atakanekiz20 • updated 17 days ago by Steve Lianoglou12k
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Comment: C: Significant but very small beta coefficients in Cox proportional hazards calcula
... Sorry my bad. Thanks for the directions. ...
written 15 months ago by atakanekiz20

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Scholar 17 months ago, created an answer that has been accepted. For A: Differences between RTCGA and TCGAbiolinks data
Scholar 17 months ago, created an answer that has been accepted. For A: GAGE analysis with the whole or a subset of matrix

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