User: atakanekiz

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atakanekiz30
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Posts by atakanekiz

<prev • 31 results • page 1 of 4 • next >
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Answer: A: Question about using sorted cell bulk microarray data (ImmGen) as reference
... Copying the response I got from Dr. Martin Hemberg (the author of the package): https://github.com/hemberg-lab/scmap/issues/19 "Hi, we have not tested scmap for mapping to bulk references, so I have no idea how well it will perform. My guess, however, is that it will not work very well as the gen ...
written 4 days ago by atakanekiz30
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Comment: C: Question about using sorted cell bulk microarray data (ImmGen) as reference
... Hi Aaron, Thanks for the info. I know about that function and I have used that already with SingleR. The reason I was asking this was a bit different. I wrote a program of my own to help with cluster annotations and I would like to compare its performance with `SingleR` and `scmap`. I would like to ...
written 4 days ago by atakanekiz30
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Question about using sorted cell bulk microarray data (ImmGen) as reference
... (cross-posted from GitHub issues page) Hello, Thanks for this helpful package. I have a question about mapping my scRNAseq data to the Immgen microarray data as the reference. As you probably already know, Immgen contains microarray data from hundreds of sorted immune cells from mice. I was able t ...
scmap written 5 days ago by atakanekiz30
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Comment: C: Understanding voom behavior when model matrix is used with/without intercept for
... Yes, my main question was about the `~x` vs `~0+x` difference when x is continuous but not when it is a factor. I'd appreciate if you could shed some light on this. I guess I'm unclear about what intercept means for factors and continuous variables at the end of the day... ...
written 10 days ago by atakanekiz30
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Comment: C: Understanding voom behavior when model matrix is used with/without intercept for
... Hi Gordon, You are right, my confusion lies in the difference of "~0+x" and "~x" when there is a continuous variable involved, but not a factor. I'm just trying to develop a better understanding of different designs. In my experience, when I was working with RNAseq data and categorical groups, diff ...
written 10 days ago by atakanekiz30
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Understanding voom behavior when model matrix is used with/without intercept for a continuous variable
... Hello, I'd like to perform DE analyses using RNAseq/microarray data and I will be using age of the patients as a continuous predictor variable. To better understand how I can do this properly, I was playing with toy data from [UC Davis](https://ucdavis-bioinformatics-training.github.io/2018-June-RN ...
rnaseq limma voom model.matrix intercept written 10 days ago by atakanekiz30 • updated 10 days ago by Gordon Smyth39k
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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 9 weeks ago by atakanekiz30
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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 weeks ago by atakanekiz30
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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 weeks ago by atakanekiz30
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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 9 weeks ago by atakanekiz30 • updated 9 weeks ago by James W. MacDonald52k

Latest awards to atakanekiz

Scholar 19 months ago, created an answer that has been accepted. For A: Differences between RTCGA and TCGAbiolinks data
Scholar 19 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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