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Graphpad Prism 1

Graphpad Prism 1. Introduction. Download & Install. You can obtain GraphPad /Prism by going to “Software Download Services” in MOLE. Look for “ Graphpad Prism for Windows or Mac”. Uniqueness of Prism.

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Graphpad Prism 1

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  1. Graphpad Prism1 Introduction

  2. Download &Install • You can obtain GraphPad/Prism by going to “Software Download Services” in MOLE. • Look for “Graphpad Prism for Windows or Mac”

  3. Uniqueness ofPrism • Prism caters for analysis and graphs forscientific publication, especially for laboratory and biomedicalresearch. • Data are usually entered and manipulated using spreadsheet such as Microsoft Excel. Data needed for analysis are copied into specifictables withinPrism. • Specific analysis requires specific tables. So you must know exactly what analysis isrequired.

  4. The 6 tables withinPrism.

  5. XY DataTables

  6. Columntables

  7. Groupedtables

  8. Contingencytables

  9. Survivaltables

  10. Parts of wholetables

  11. Choosing theappropriate statisticaltests Use these tables to choosethe appropriate statisticaltests.

  12. Parametric StatisticalTests Independent Dependent Test

  13. Non-parametric StatisticalTests Independent Dependent Test

  14. Statistical Tests for QualitativeData

  15. Data – Factors Related toSGA

  16. A study to identify factors that can cause small for gestational age (SGA) was conducted. Among the factors studied were the mothers’bodymassindex(BMI).It is believedthatmotherswith lower BMI were of higher risk to getSGA babies. • 1. Create a new variable mBMI (Mothers’ Body Mass Index) from the mothers’ HEIGHT (in metre) & WEIGHT (first trimester weight in kg). mBMI = weightin kg/(height in metre)2. Calculate the following formBMI; • Mean • Standarddeviation • 2. Create a new variable OBESCLAS (Classification of Obesity) from mBMI.Use the following cutoffpoint; • <20 =Underweight • – 20 – 24.99 =Normal • 25 or larger =Overweight • Create a frequency table forOBESCLAS. • 3. Conduct the appropriate statisticaltest to test whether there is any association between OBESCLAS (Underweight/ Normal/Overweight) andOUTCOME. • 4. Conduct the appropriate statisticaltest to test whether there is any association between BMI andOUTCOME. • 5. Conduct the appropriate statistical test to find any association betweenOBESCLAS (Underweight/Normal/Overweight) and BIRTHWGT. • 6. Assuming that both variables mBMI& BIRTHWGT are normally distributed, conduct an appropriate statistical testto prove the association between the two variables. • – Demonstrate the association usingthe appropriate chart. Determine the coefficient ofdetermination. • 7. Conduct Simple Linear Regression using BIRTHWGT as the dependent variable. Try to come out with a formula that will predict the baby’s birthweight based on the mother’sBMI. – y = a +bx

  17. Exercise 1 &2 • 1. Create a new variable mBMI (Mothers’ Body Mass Index) from the mothers’ HEIGHT (in metre) & WEIGHT (first trimester weight in kg). mBMI = weight in kg/(height in metre)2. Calculate the following formBMI; • Mean • Standarddeviation • 2. Create a new variable OBESCLAS (Classification of Obesity) from mBMI. Use the following cutoffpoint; • <20 =Underweight • – 20 – 24.99 =Normal • 25 or larger =Overweight • Create a frequency table forOBESCLAS.

  18. ComputeBMI Drag down to fill up thecells

  19. Recode BMI intoOBESCLAS • Type • =IF(F2<20,"Underweigh t",IF(F2>25,"Overweight ","Normal")) in cell G2 and pressEnter. • Then drag down cellG2 until G101 to fill up the rest of thecells. • Try to “understand” the code below: • If (“condition 1 satisfied” ,then put Value 1,otherwise put Value2). (Comma is very important here!) • Instead of Value 2 you can introduce another IF! Can you see how it works?

  20. Recode BMI intoOBESCLAS

  21. Recode BMI into 1,2 or3 • We should also recode BMI into numeric OBESCLAS2 for import into Prism. Prismdoesn’t accept stringdata. • • =IF(F2<20,“1",IF(F2>25,“3 • ",“2")) in cell H2 andpress Enter. • Then drag down cellH2 untilH101tofillupthe rest of thecells.

  22. Pivot Table: Frequency (Count) of data by category of BMI • Select column “OBESCLAS” • Click “Insert” -> “Pivot Table” • Click OK and it will open a new sheet in Excel. • Drag “OBESCLAS” in “Row” once. • Drag “OBESCLAS” in Sigma value. • You will see a table of count of data. • To switch to percentage, you can right click on one cell of the tableand “show value as percentage Total”. • You can create a Pie chart by clicking on the table and going in Pie Chart. • You can also right click on one of the slices of the Pie Chart and click on “Add Data Labels”. • You can also modify the title of the graph by clicking on “Total” and changing the text.

  23. Import Excel Data IntoPrism • Selectallthedatafrom• • Excel.Copy. Open Prism, select “Columns”, “Enter replicate values..”& click“Create”

  24. Paste IntoPrism • Click the cellbetween “Group A” and row Y andpaste. drtamil@gmail.com

  25. CheckingNormality • Click on the“Analyze” button. • Select“Column Statistics”. • Select the variables with continuousdata. • Then click“OK”.

  26. Click on thefollowing; • Test if the values from a Gaussian distribution.

  27. Only Height is normallydistributed But for the purpose of today’s exercise, we are going toASS-U-ME that all these continuous variables are normallydistributed.

  28. Question 1 –BMI • Column Statistics also generates the Mean& S.D.; • – Mean24.49 • – S.D.4.769

  29. FrequencyDistribution • Go back to the databy clicking on the data table on left side of screen. Then click on the “Analyze” button again. • Select“Frequency Distribution” • Tick onOBESCLAS2. Then click on“OK”.

  30. FrequencyDistribution • Then click on OK again. You will get the following frequency distributiontable.

  31. Question 2 – ObeseClassification • UW –17% • N –40% • OW –43%

  32. Exercise 3 • 3. Conduct the appropriate statistical test to test whether there is anyassociation betweenOBESCLAS TOTAL 50 50 100 • (Underweight/Normal/ Overweight) and OUTCOME. • Therefore mostsuitable analysis is Pearson Chi- square.

  33. Pivot Table inExcel • Click on “Insert”,“Pivot Table” inExcel. • Select all yourearlier Exceldata.

  34. PivotTable • On the right side of the screen, pull FREQ into values, OBESCLAS into row labels and OUTCOME into column labels. • Now select the created contingency table(excluding the “Grand Total”), and copy itusing Ctrl-C.

  35. Paste Pivot Table IntoPrism • Click “New”, “NewData Table”. • Select “Contingency”, “Start with an empty table”. • Then paste thepivot table intoPrism.

  36. The Pasted Pivot Table

  37. Chi-SquareAnalysis • Click on “Analyze”,“Contingency table analysis”, then “Chi- square”, then OK againtwice.

  38. Chi-Square Results fromPrism Contingency 60 SGA Normal 40 Frequency 20 0 Normal OverweightUnderweight Mothers' WeightClassification • Prism only states that there is a significant association(p • < 0.0001) between mother’s weight classificationand small for gestationalage. • Butitdoesn’tshowwhichgrouphasthehigherrateof SGA.

  39. Combine Results From Excel &Prism • There is a significant difference (p<0.0001) of SGA rates between underweight, normal and overweightmothers. • Underweight mothers has a higher rate (94%) ofSGA, compared to normal mothers (58%) and overweight mothers(26%).

  40. Underweight vsNormal? • There is a significant difference (p<0.01) of SGA rates between underweight and normalmothers. • Underweight mothers has a significantly higherrate (94%) of SGA, compared to normal mothers(58%).

  41. Question3

  42. Question3

  43. Exercise 4 • 4. Conduct the appropriate statisticaltest to test whether there is any association between BMI andOUTCOME. • Basically we are comparing the meanBMI of SGA mothers against BMI of Normalmothers. • Therefore theappropriate test is Student’st-test. Independent Dependent Test

  44. Copy BMI Column IntoPrism • Click “New”, “NewData Table”. • Select “Column”, “Enter replicate values intostacked columns”. • Then paste the BMI of SGA mothers into column A & BMI of Normal mothersinto columnB.

  45. The Pasted BMIData

  46. Click on “Analyze”, “Column analysis”, then “t-tests”,then OKagain. Student’sT-Test • Tick “Unpaired”, “Yes, parametric”, then “equalSDs”, then OKagain.

  47. T-Test Results fromPrism • Prism states that thereis a significant mean difference of BMI (p < 0.0001) between SGA mother’s (22.52) and normal mothers (26.46). Therefore mean BMI of SGA mothers is significantly lower than the normalmothers. • And it also proves that there is equal variancesof the twomeans.

  48. BMI

  49. Question4

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