User: pixie@bioinfo

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pixie@bioinfo1.3k
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PhD Student

Posts by pixie@bioinfo

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Comment: C: DESeq2- R commands for multiple groups
... Hi Devon, one last query. I am also interested in constructing co-expression networks with the rlog transformed data. `rlogged_data <- rlog(ds2)` How do I export rlogged_data object as a matrix (text or csv) for further analysis in WGCNA ? Thanks ...
written 11 weeks ago by pixie@bioinfo1.3k
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Comment: C: DESeq2- R commands for multiple groups
... Yes, I started with the DESeq2 paper, but the kept referring to the previous paper so had to read that one to get an idea. ...
written 12 weeks ago by pixie@bioinfo1.3k
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Comment: C: DESeq2- R commands for multiple groups
... Thanks a lot for the input ! ...
written 12 weeks ago by pixie@bioinfo1.3k
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Comment: C: RefSeq and mRNA
... You have any IDs or any disease/organism of interest ? You need to search based on that and the technology used. ...
written 12 weeks ago by pixie@bioinfo1.3k
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Comment: C: DESeq2- R commands for multiple groups
... Hi Devon, I was going through the DESeq (and DESeq2) papers to understand the models they are using, and also because I am a novice in this field. In the paper, they are calculating the size-factor which is explained here : http://seqanswers.com/forums/showpost.php?p=16468&postcount=13 So in my ...
written 12 weeks ago by pixie@bioinfo1.3k
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Comment: C: DESeq2- R commands for multiple groups
... Thanks for the pointers. I will try that out ...
written 12 weeks ago by pixie@bioinfo1.3k
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DESeq2- R commands for multiple groups
... My RNA-seq read count table consists of samples fro two tissues (root and shoot), different time-points (1hr, 3hr, 12hr, 1day etc). and stress and no-stress conditions all in one table. For example: `root_ctrl_rep1 root_ctrl_rep2 root_1hr_rep1 root_1hr_rep2 root_3hr_rep1 root_3hr ...
deseq2 rna-seq written 12 weeks ago by pixie@bioinfo1.3k
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Comment: C: Suggestions regarding bioinformatics journal
... Thanks. Yup, the show must go on :) ...
written 4 months ago by pixie@bioinfo1.3k
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Comment: C: Suggestions regarding bioinformatics journal
... Thanks, yes we are going to do that now. ...
written 4 months ago by pixie@bioinfo1.3k
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Comment: C: Suggestions regarding bioinformatics journal
... Okay, point noted :) ...
written 4 months ago by pixie@bioinfo1.3k

Latest awards to pixie@bioinfo

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