User: Vasu

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Vasu340
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Posts by Vasu

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Identification of transcription factor - gene regulation information
... I have seen many databases like TRANSFAC, HTRIdb, TRRUST etc..from where I can download information about TF-gene regulation in different cancer datasets. But I'm interested in finding TF-gene regulation information specific to the samples I'm working with. I have ER+ samples of TCGA Breast cancer ...
transcription factor tcga rna-seq written 9 weeks ago by Vasu340 • updated 9 weeks ago by ATpoint19k
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Comment: C: Question about chromosomal instability
... Yes sure. Thanks a lot. And Z > +/- 1.96 (roughly p=0.05 or 2 SD away) ...
written 11 weeks ago by Vasu340
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Comment: C: Question about chromosomal instability
... I have the FPKM expression of that gene with 370 samples. How to classify them into high and low groups? ...
written 11 weeks ago by Vasu340
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Comment: C: Question about chromosomal instability
... The specific gene I'm interested in is `CENPH`. For chromosomal instability Do you think the following way is right? I have the gistic2 thresholded gene level Copy number data. Classifying samples into `CENPH` high and `CENPH` low groups. And then checking the % of genes which are not 0. Do you th ...
written 11 weeks ago by Vasu340
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Comment: C: Question about differentially expressed genes selection for low sample size data
... Thanks a lot for clear explanation shawn. ...
written 11 weeks ago by Vasu340
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Comment: C: Question about differentially expressed genes selection for low sample size data
... Hey Kevin so what is your opinion on this finally? ...
written 11 weeks ago by Vasu340
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Comment: C: Question about differentially expressed genes selection for low sample size data
... Thanks a lot for the answer shawn. I am aware that FDR is adjusted pvalue but dont know why pvalue is not used for significance instead of adjusted pvalue. If you dont mind could you please tell me exact reason why significance is based on FDR and not pvalue? ...
written 11 weeks ago by Vasu340
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Question about differentially expressed genes selection for low sample size data
... I am using egdeR for differential analysis. It is between gene TULP4 silenced cell-line vs controls. As the sample size is very low 4 shTULP4 and 4 Controls, (shTULP4 vs Controls), I'm selecting differentially expressed genes only based on FDR < 0.05. In this analysis I'm very much interested ...
pvalue edger geneexpression rna-seq R written 11 weeks ago by Vasu340 • updated 11 weeks ago by shawn.w.foley780
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Question about chromosomal instability
... I have copy number data. I'm interested in measuring chromosomal instability of a specific gene computational way. Are there any tools or packages to measure the chromosomal instability? tools and packages are really required for this? Can anyone help me out how to check the chromosomal instabilit ...
gene R chromosome copy number genome written 3 months ago by Vasu340 • updated 3 months ago by Kevin Blighe46k
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Comment: C: Question about ClinicalData discrepancies b/w cbioportal data and GDC data?
... I see the patients are same in both the portals. From the same place where I downloaded patient clinical data for both colon and rectal in GDC, I have also downloaded the following files nationwidechildrens.org_clinical_follow_up_v1.0_coad.txt nationwidechildrens.org_clinical_follow_ ...
written 4 months ago by Vasu340

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Popular Question 4 weeks ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
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