User: maziz@tgen.org

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Posts by maziz@tgen.org

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Answer: A: Question regarding cellhts2 output
... Thanks Joseph for answering all my questions. I am trying to compare the outputs from "negative" control based normalization and simply the zscore (median) non-control based normalization. For non-control based normalization I understand that the raw value is subtracted from the median of the all th ...
written 6.6 years ago by maziz@tgen.org70
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Answer: A: Question regarding cellhts2 output
... Hi Joseph, If we are using the following: Documentation: ## robust Z score method (plate intensities are subtracted by the per- plate median on sample wells and divided by the per-plate MAD on sample wells): xZ <- normalizePlates(KcViabSmall, scale="additive", log=FALSE, method="median", va ...
written 6.6 years ago by maziz@tgen.org70
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Question regarding cellhts2 output
... Hi, Will CellHTS2 work if I donot have positive controls on my plate. I only have negative controls. Thanks, Meraj -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of maziz@tgen.org Sent: Saturday, July 28, 2012 12:11 PM To: ...
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Answer: A: Question regarding cellhts2 output
... Hi Joseph, We are getting ready to writeup our findings. I am still wondering about one question. I apologize if you have answered that before But in order to clarify please help me understand the process by which CellHTS2 processes out data. So as I mentioned before we have 900 siRNA (x4 siRNA pe ...
written 7.3 years ago by maziz@tgen.org70
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Question regarding cellhts2 output
... Thank you for responding. Somehow I did not receive your reply email and I got to your response to my question when I was searching for a solution online. So given the variances are accounted for: According to wikipedia: FPR = FP/(FP+TN) Suppose I have 50 wells of "-ve" controls in total across a ...
normalization cellhts2 assign written 7.3 years ago by maziz@tgen.org70
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Answer: A: Question regarding cellhts2 output
... I am using CellHTS2 to calculate Bscores. My experiment has only one replicate. There are approx 900 genes (x4 siRNA). From: Meraj Aziz Sent: Saturday, June 16, 2012 5:05 PM To: 'Joseph Barry' Cc: 'bioconductor@r-project.org' Subject: RE: Question regarding cellhts2 output Hi, Is there a way to c ...
written 7.4 years ago by maziz@tgen.org70
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Answer: A: Question regarding cellhts2 output
... Hi, Is there a way to calculate the False Discovery Rate (FDR) for an RNAi Experiment. Thanks, Meraj From: Joseph Barry [mailto:joseph.barry@embl.de] Sent: Wednesday, June 13, 2012 2:45 PM To: Meraj Aziz Subject: Re: Question regarding cellhts2 output Hi Meraj, Yes, that would be great. Thanks ...
written 7.4 years ago by maziz@tgen.org70

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