User: Antony

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Antony0
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Posts by Antony

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Comment: C: Top gene expression values in RNA Seq
... Ok, that's great. Thanks, I'll look into those. This is all very new to me and I work down to the wire so I don't have much time to learn and pick up the techniques. I had the impression that there was (for want of a better word) an intermediate QC stage i.e., how do the samples sit across varying ...
written 26 days ago by Antony0
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Comment: C: Top gene expression values in RNA Seq
... Right I see. That is quite helpful to know. So, I have actually completed a complete DESeq2 analysis, however, the recommendation I've had from a Prof in Bioinformatics that I work with (very off hand due to distance and hence my posts here), isn't interested in any end-game outcome until a thorough ...
written 26 days ago by Antony0
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Comment: C: Top gene expression values in RNA Seq
... Oh I see. Not a problem. This is all cell samples from mice. I do not expect the treatment to cause cell lysis/up-regulate mitochondrial gene expression (the latter, at least as far as I know). These are not selected after DESeq2. This is the QC analysis from Scater immediately after counts are im ...
written 26 days ago by Antony0
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Comment: C: Top gene expression values in RNA Seq
... Thanks. I've added the experimental metadata into the post. As for the various tools, thanks for that. I'm trying to keep the number of tools to a minimum as it' a bit overwhelming at the moment, reminds me of the basis-set alphabet soup in QM chemistry. ...
written 26 days ago by Antony0
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Top gene expression values in RNA Seq
... I am a comp-chemist and this is my first time trying RNA and I have little in the way of support in biology. The experiment is a mouse model (mouse cells were sequenced and I ended up with bulk paired-end reads) over 30 days, control vs treated. The experimental metadata: **Sample_ID Duration ...
rna-seq written 26 days ago by Antony0
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How to retrieve gene expression values from L1000 signatures?
... I am trying to retrieve up/down gene expression scores using the LINCS L1000 landmark gene set. I have the gctx and csv files provided from the L1000FWD page: http://amp.pharm.mssm.edu/l1000fwd/download_page I am able to retrieve the list of significantly differentially expressed genes from the CD ...
expression lincs l1000 written 29 days ago by Antony0
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Comment: C: How to cluster drugs by up/down gene lists?
... I now have the complete gene list and I am taking the approach of +1 (up), 0 (missing), -1 (down). When I find a means of calculating a similarity/distance, I'll edit my post. Thanks. ...
written 4 weeks ago by Antony0
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Comment: C: How to cluster drugs by up/down gene lists?
... Thanks for all of the information. I work down to the wire, but when I've looked into this wealth of information I'll reply. ...
written 4 weeks ago by Antony0
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Comment: C: How to cluster drugs by up/down gene lists?
... Thanks, Jean-Karim. I'll give it a try. Just an added thought, I'm struggling to visualise how this is going to work if the genes expressed between drugs are different for example, just looking at up genes, how would two vectors be comparable if in the same element position they had a "1" but for t ...
written 5 weeks ago by Antony0
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How to cluster drugs by up/down gene lists?
... I'm hoping for some help on drug clustering by gene list. The data I have has not come through any particular workflow, it's all held in text files. I have a 100 drugs and per drug I have a list up/down genes. Whether a gene is up/down regulated is purely by its presence in a text file (as two col ...
gene drug clustering written 5 weeks ago by Antony0 • updated 5 weeks ago by Jean-Karim Heriche18k

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