fold change analysis

More Aparna Sampath's questions See All

Selecting genes based on highest variance across samples

Hi I was stuck while trying to get the top genes that had the highest expression variance across patients. I have a gene expression data and I would like to choose only lets say top 200 genes...

05 June 2011 4,306 0 View

Normalization of gene expression data

Hi All I came across this paper which does normalization of both rows and columns, and as far as I know we cannot normalize rows and columns simultaneously and also most people prefer to either...

04 May 2011 3,898 6 View

Help on R language for biostatistics

Hi All I am completely new to R and I am currently working on a project using R. I would like to know, how do we normalize using R for gene expression data.

04 May 2011 3,554 1 View

Normalization of both rows and columns in gene expression data

Hi All Normalization is very important for clustering gene expression data. I am working on some cancer-related datasets and I came across this paper which does normalization of both rows and...

04 May 2011 6,876 10 View

PERL programming for Bioinformatics

Hi all, I see the use of PERL is largely dominating the research field these days, and as a fresh graduate, I think it is important to get hands-on experience in PERL programming for better...

01 February 2011 2,678 2 View

Gene expression analysis- time course data

Anyone has any idea about pvalue and fold change in gene expression analysis?

06 July 2010 6,125 11 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

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MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

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MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

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MGL tools

20 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

i have some problem with chtMultiRegionSimpleFoam

--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

24 March 2021 0 0 View

Alexei Levitchi

can you be more clear?

you need to extract data from the second tool and make it "manually"

Amit Kumar Banerjee

Reply for Aparna's query

Dear Aparna,

In general belief if you are comparing two tools, parameters should be same for both, moreover if one is accepting negative data and the other not(where you do have negative data in your data set) then there is no logic of comparing the tools as you cannot conclude their performances in a unbiased manner.