User: JackieMe

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JackieMe0
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Posts by JackieMe

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Need help determine optimal argument value on a rbsurv model
... I am using the rbsurv packaeg to select surival-assosiated probes. My data was pre-processed microarray data with ~7,000 probes and 192 tumor samples. Data was split in half for modeling and validation(train and test data).  I also included in my model a risk predictor, tumor stage, to help model fi ...
microarray survival rbsurv written 17 hours ago by JackieMe0
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Comment: C: Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene an
... Thanks! That's exactly what I am looking for. ...
written 11 days ago by JackieMe0
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Comment: C: Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene an
... Thank you Gordon! I am sorry if I am asking some strange questions. In addition to this, multiple mapping ( dual probes mapping to a gene ) is common in hgu133plus array. I've seen some posts online said that to replace the expression values of the probes with thier mean/max expression values.     ...
written 11 days ago by JackieMe0
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Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
... I am learning to do differentially expressed gene analysis on microarray data(typically Affaymetrix GeneChip Human Genome U133 Plus 2.0 Array) of tumor vs normal. I've read some tutorials and know the basic steps. But I never saw people talk about when exactly to annotate the probes to gene symbols. ...
microarray limma deg written 12 days ago by JackieMe0 • updated 11 days ago by Gordon Smyth32k
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Comment: C: DESeq2/edgeR DEG analysis data input from TCGA and correation analysis
... Thanks for your reply, Aaron! I saw your answer days ago and realized I haven't understand how edgeR works so I went back reading the edgeR User Guild, took me a while to get a glimpse of the capability and usage of edgeR. To answer your suggestion: Yes, I already filtered low-abundance genes out ...
written 14 days ago by JackieMe0
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Answer: A: How to permanently add custom repositories to BiocLite
... Do you mean a local repo on your own computer? That I don't know, maybe this thread is helpful. In case you mean another Bioconductor website, put the something like following line in your ~/.Rprofile :   options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor")   This sets the Bi ...
written 27 days ago by JackieMe0
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DESeq2/edgeR DEG analysis data input from TCGA and correation analysis
... Hello alll. I am a newbie in bioinformatics and still learning. The thing is, I want to do differential expressed gene(DEG) analysis in the TCGA RNA-seq data. DESeq2 and edgeR manuals said they require raw count data as input, so I downloaded STAD.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3 ...
edger tcga written 27 days ago by JackieMe0 • updated 25 days ago by Aaron Lun16k

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