Science Forums Biology Forum Molecular Biology Forum Physics Chemistry Forum Chi-Squared doesn't work!!
 User Name Remember Me? Password

 BioStatistics Forum Post Questions and Discuss Biostatistics Programs and Stastistical Analysis Questions

# Chi-Squared doesn't work!!

## Chi-Squared doesn't work!! - BioStatistics Forum

### Chi-Squared doesn't work!! - Post Questions and Discuss Biostatistics Programs and Stastistical Analysis Questions

#1
08-09-2011, 07:04 AM
Pipette Filler

Join Date: Aug 2011
Posts: 2
Thanks: 0
Thanked 0 Times in 0 Posts
Chi-Squared doesn't work!!

Hey guys

I need to do a Chi-Squared between two sequence and their reference.

I have a table of 2 columns and 2 rows.
column 1 : cell type 1
column 2 : cell type 2
row 1 : reference nucleotide
row 2 : mutation (SNP)

I wanna know if the difference between the reference and mutation is significant. So we counted the number of read (from sequencer) aligned to the reference and the mutation.

In this objective, I decided to do a Chi-squared with a 2x2 Contingency table with the following formula:
(AD-BC)^2 . N
(A+B)(C+D)(A+C)(B+D)

The problem is everytime that we have a de novo SNP with no read aligned (value 0) to the reference the chi-squared and p-value are returned as null (coz with this formulas you cannot time by 0).
For example if
A=0
B=0
C=22
D=239
==> FOR US this means that we have a de novo SNPs so it is significant. BUT X^2 RETURNS a value of 0...

Does anyone has a better idea to improve my method of finding de novo and significant mutation ?

Thanks

Abbreviations used in X^2 table :
ROW 1 / CELL 1 : A
ROW 1 / CELL 2 : B
ROW 2 / CELL 1 : C
ROW 2 / CELL 2 : D

A + B + C + D = N

 Tags chisquared , work

 Thread Tools Display Modes Linear Mode

 Posting Rules You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is OffTrackbacks are On Pingbacks are On Refbacks are On Forum Rules
 Forum Jump User Control Panel Private Messages Subscriptions Who's Online Search Forums Forums Home General Science Forums     Biology Forum     New Member Introductions Forum     Chemistry Forum         Organic Chemistry Forum     Physics Forum     General Science Questions and Layperson Board         Science and Religion Forum         Zoology Forum     Environmental Sciences and Issues General Forum     Chit Chat         Science and Lab Jokes     Article Discussion     Molecular Biology News and Announcements         Conferences , Symposiums and Meetings         Molecular Station Suggestion Forum         Instructions for Posting, Help, and Frequently Asked Questions     Science News and Views         Molecular Biology Lectures and Videos     Science Careers         Post-doctoral         Medical School         Ph.D Doctor of Philosophy         Science Jobs Forum Molecular Research Topics Forum     PCR - Polymerase Chain Reaction Forum         Real-Time PCR and Quantitative PCR Forum     Bioinformatics         BioStatistics Forum     Molecular Biology Techniques         Molecular Cloning Forum         Electrophoretic Mobility Shift Assay Forum         Agarose Gel Electrophoresis Forum         BioPhysics Forum         Gene Therapy     Cell Biology and Cell Culture         Apoptosis, Autophagy, and Necrosis Forum         Flow Cytometry Forum         Transfection Forum         Confocal - Microscopy Imaging Techniques         Immunology and Host-Pathogen Interactions         Signalling Biology         Stem Cell Forum     Basic Lab Protocols and Techniques         SDS-PAGE Gel Electrophoresis Forum     DNA Techniques         DNA Extraction Forum         cDNA Forum     Epigenetics Forum: DNA Methylation, Histone and Chromatin Study         ChIP Chromatin Immunoprecipitation Forum     Protein Science         Antibody Forum             Immunoprecipitation Forum         Western Blot Forum         Protein Crystallography Forum         Recombinant Protein Forum         ELISA Assay Forum         Protein Forum     Proteomics Forum         Peptide Forum         Mass Spectrometry Forum         2-D Gel Electrophoresis Forum     Omics and Genomics Forum         Microarrays Forum         Genomics Forum     RNA Techniques Forum         RNAi and SiRNA Forum     Histology Forum         Immunohistochemistry Forum         Immunocytochemistry Forum         Electron Microscopy Forum         Immunofluorescence Forum     Protocols and Methods Forum     Molecular Biology Articles and Protocols     Animal and Molecular Model Systems         Drosophila Forum         Yeast Forum         Zebrafish Forum         Botany Forum         C Elegans Forum         Arabidopsis and Plant Biology         Microbiology Forum         Knockout Mouse Forum     Chromatography Forum Products and Vendor Discussion     Molecular Biology Products and Vendors         Bad Product/Service? Post Here         Lab Equipment Discussion and Reviews Regional Molecular Biology Discussion     Forum Chemie     Forum Biologie     Forum Biologia     Forum Chimica     Forum Physik     Forum De Chimie     Forum De Physique     Forum Chemia     中国人分子的生物学论坛 Chinese     Greek Molecular Biology Forums     分子生物学のフォーラム Japanese     ميدان فارسى. Persian Molecular Biology     [أربيك] علم ساحة- Arabic     Forum de Biologie Moleculaire     Forum Biologia Molecolare     Forum die Molekularbiologie     Foro Biologia Molecular

 Similar Threads Thread Thread Starter Forum Replies Last Post Robert Physics Forum 2 01-04-2008 11:50 AM jon_johnfrancisayres@yahoo.com Microbiology Forum 0 10-06-2007 05:59 AM Peter Van Osta Cell Biology and Cell Culture 0 01-06-2005 10:18 AM cinquirer Physics Forum 42 11-25-2003 06:58 PM

All times are GMT. The time now is 09:13 AM.

 Contact Us - Molecular Biology - Archive - Privacy Statement - Top

Powered by vBulletin® Version 3.8.4
Copyright ©2000 - 2013, Jelsoft Enterprises Ltd.
Copyright 2005 - 2012 Molecular Station | All Rights Reserved
Page generated in 0.19110 seconds with 16 queries