# BIOL398-03/S13:Class Journal Week 9

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 Revision as of 18:08, 2 April 2013 (view source)← Previous diff Current revision (04:06, 3 April 2013) (view source) (11 intermediate revisions not shown.) Line 34: Line 34: #*Looking at and analyzing the data definitely helped me to understand it more. I was having a hard time trying to figure out how the data was normalized, so going through the process cleared that up. I am also a big number person, so this was a good assignment for me. #*Looking at and analyzing the data definitely helped me to understand it more. I was having a hard time trying to figure out how the data was normalized, so going through the process cleared that up. I am also a big number person, so this was a good assignment for me. [[User:Kasey E. O'Connor|Kasey E. O'Connor]] 18:08, 2 April 2013 (EDT) [[User:Kasey E. O'Connor|Kasey E. O'Connor]] 18:08, 2 April 2013 (EDT) + + ==James P. McDonald Week 9 Journal== + [[User:James P. McDonald|James P. McDonald]] + + #What aspect of this assignment came most easily to you? + #*Finding the averages and standard deviations of the data using the excel formulas came the easiest to me. + #What aspect of this assignment was the most challenging for you? + #*Using the filtering function for the sanity check was challenging at first because it was the first time I had ever used it. + #What (yet) do you not understand? + #*There was no part of this assignment that I did not understand because the instructions were straightforward. + #Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not? + #*I was initially unsure how the massive amounts produced by microarrays were analyzed but I now understand how this data can be organized efficiently. + + [[User:James P. McDonald|James P. McDonald]] 21:02, 2 April 2013 (EDT) + + ==Helena M. Olivieri Week 9 Journal== + [[User:Helena M. Olivieri|Helena M. Olivieri]] + #What aspect of this assignment came most easily to you? + #*The simple statistical analysis came the most easily. + #What aspect of this assignment was the most challenging for you? + #*If you don't keep the data organized and stay focused, it becomes very easy to make a simple mistake. So I suppose, staying engaged in the number "crunching" can be a little challenging. + #What (yet) do you not understand? + #*How we are going to analyze and compare our data when looking at more than one microarray data set. + #Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not? + #*So far, "crunching" the data has been a good hands on way to understand microarray experiments and data. But, the work is very tedious and after a while it becomes a little difficult not to become somewhat robotic. + [[User:Helena M. Olivieri|Helena M. Olivieri]] 21:32, 2 April 2013 (EDT) + + ==Matthew E. Jurek Week 9== + [[User: Matthew E. Jurek| Matthew E. Jurek]] + #What aspect of this assignment came most easily to you? + #*I found that the basic Excel functions came most easily to me.  Taking averages and creating the basic formulas within Excel wasn't too difficult. + #What aspect of this assignment was the most challenging for you? + #*The hardest part was working with such a large spreadsheet.  I've never worked with a sheet this large.  It was easy to lose my place or mix up columns.  Working with such a wide array of data was challenging at times. + #What (yet) do you not understand? + #*I'm not sure I did the Bonferroni correction properly.  Following the correction, I had zero p values that were less then .05 across all time points.  Based on the questions following the correction I feel that's wrong.  I checked my work a few times and still found zero p values in that range.  I understand what the correction is geared towards, but I'm not sure it worked properly on my spreadsheet. + #Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not? + #*It appears a majority of the experiment is "crunching" numbers on a spreadsheet.  Seeing that I just did this crunching, I would say I've done a majority of the experiment.  Since these experiments are so data intensive, I feel I have a better understanding. + + *'''[[User:Matthew E. Jurek|Matthew E. Jurek]] 22:47, 2 April 2013 (EDT)''': + + ==Salman Ahmad Week 9 Journal== + [[User:Salman Ahmad|Salman Ahmad]] + #What aspect of this assignment came most easily to you? + #*It was pretty easy to follow along in class and do the parts of the assignment we went over. + #What aspect of this assignment was the most challenging for you? + #*It was hard to keep everything straight. I ended up getting a few strange results, so I had to go back and do it a few times before it ended up being correct. + #What (yet) do you not understand? + #*I don't understand the reasoning behind the Bonferroni correction. It seems like it is unlikely to have many p-values after doing the calculation. + #Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not? + #*Yes. I now realize that working out all of the numbers is how to actually interpret the results from a microarray. It is easier to see now how specific genes can be picked out from the other thousands of genes that we are looking at. + [[User:Salman Ahmad|Salman Ahmad]] 00:28, 3 April 2013 (EDT) + + ==Elizabeth Polidan Week 9 Journal== + [[User:Elizabeth Polidan|Elizabeth Polidan]] + + #What aspect of this assignment came most easily to you? + #*The manipulations in Excel were easiest.  I have used this software often. + #What aspect of this assignment was the most challenging for you? + #*Even though I was able to manipulate the data with ease, I am concerned about one of my answers.  I found the gene with the smallest p-value is a gene whose function is unknown.  I am not sure that was the intended gene. + #What (yet) do you not understand? + #*Other than what I did wrong, it's pretty straightforward. + #Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not? + #*I think it is the best way to really get to know what the process is all about.  I do believe that the College of Science and Engineering should seriously consider some way of getting students familiar with more intricate manipulations in Excel, SPSS, etc. earlier in their academic career. + + [[User:Elizabeth Polidan|Elizabeth Polidan]] 01:41, 3 April 2013 (EDT) + + ==Paul Magnano Week 9 Journal== + [[User:Paul Magnano|Paul Magnano]] + + #What aspect of this assignment came most easily to you? + #*Manipulating the data was the easiest part, because of the straight forward directions. All that you had to do was enter the formulas correctly. + #What aspect of this assignment was the most challenging for you? + #*The sanity check was confusing simply because it seemed that my data manipulations were incorrect, but after checking my spreadsheet formulas and seeing they were correct, it made sense. + #What (yet) do you not understand? + #*Nothing I understood why we were doing everything since it was explained in class as we did the manipulations. + #Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not? + #*Yes, before it seemed very hard considering the entire genome is being analyzed (in this case over 6000 genes) but after seeing how the data is organized I can see that as long as it is done carefully the experiment would be relatively straightforward. + [[User:Paul Magnano|Paul Magnano]] 01:50, 3 April 2013 (EDT) + + ==Anthony J. Wavrin Week 9 Journal== + [[User:Anthony J. Wavrin|Anthony J. Wavrin]] + + #What aspect of this assignment came most easily to you? + #*The statistics portion, being involved in research for a few years has given me a lot of exposure to statistics and how it can be used, and misused, to show data.  Thus, manipulating the p values and log changes to see how many genes had a large change in expression was a good example of going being the “significant” value. + #What aspect of this assignment was the most challenging for you? + #*The actual manipulation and sorting on the excel sheet.  It was so much challenging as it was more grunt work that took time.  I know that it is necessary but, it is not a very enjoying, nor stimulating activity. + #What (yet) do you not understand? + #*With regards to understanding DNA microarrays and statistics, I am fairly comfortable with those subjects.  However, I have no idea how we are supposed to model all of this not just mathematically difficult but, the 6189 genes and trying to model all of them correctly is was I do not understand. + #Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not? + #*I think that it may have helped me understand it if I had never done anything like it before but, since I am in both of your classes and went to your lecture during convo, I felt like I had a very good grasp of the concept before this assignment. + [[User:Anthony J. Wavrin|Anthony J. Wavrin]] 02:32, 3 April 2013 (EDT) + + ==Ashley Rhoades Week == + [[User:Ashley Rhoades|Ashley Rhoades]] + ===Reflection=== + #What aspect of this assignment came most easily to you? + #*Looking through and reflecting on the data after sorting through it. + #What aspect of this assignment was the most challenging for you? + #*The most challenging aspect was keeping myself organized with all the columns of data. + #What (yet) do you not understand? + #*There is nothing I really don't understand, but I realize this is just the beginning of the project. + #Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not? + #*For me it does help me understand the data better. I like statistics so this gave me an opportunity to look at the data through a familiar lens. + [[User:Ashley Rhoades|Ashley Rhoades]] 04:06, 3 April 2013 (EDT)

# Reflection

## Laura Terada Week 3 Journal

### Reflection

1. What aspect of this assignment came most easily to you?
• Doing the basic excel functions came the easiest to me (ex: average, stdev).
2. What aspect of this assignment was the most challenging for you?
• The most challenging part was in the sanity check section where we had to use all the filters, since I have never used that feature before.
3. What (yet) do you not understand?
• Nothing- the assignment was pretty straightforward!
4. Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not?
• It doesn't help me to understand the experiment better, but it also doesn't NOT help me. I understood microarray experiments before this assignment; however, I suppose this helps me in developing the skills needed to deal with raw data.

Laura Terada 14:20, 2 April 2013 (EDT)

1. None of it came easily for me.
2. Using excel is hard for me and was very time consuming with the tediousness of this assignment,.
3. I need to review the statistics material, I had stats last semester but have apparently not retained much of what I learned.
4. No, I could have gained the same knowledghe I did during this assignment seeing a worksheet with everything already performed, doing this just took a lot of time.

Kevin Matthew McKay 15:10, 2 April 2013 (EDT)

## Kasey E. O'Connor Week 3 Journal

### Reflection

1. What aspect of this assignment came most easily to you?
• Sorting all the data and filtering came the easiest to me.
2. What aspect of this assignment was the most challenging for you?
• The most challenging part of the assignment was keeping all the columns straight because there were so many. Making sure that I was using the correct column and row for each equation got a little confusing with all of the data.
3. What (yet) do you not understand?
• There is nothing that I did not understand, it was a very easy assignment to follow because it was laid out so well.
4. Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not?
• Looking at and analyzing the data definitely helped me to understand it more. I was having a hard time trying to figure out how the data was normalized, so going through the process cleared that up. I am also a big number person, so this was a good assignment for me.

Kasey E. O'Connor 18:08, 2 April 2013 (EDT)

## James P. McDonald Week 9 Journal

1. What aspect of this assignment came most easily to you?
• Finding the averages and standard deviations of the data using the excel formulas came the easiest to me.
2. What aspect of this assignment was the most challenging for you?
• Using the filtering function for the sanity check was challenging at first because it was the first time I had ever used it.
3. What (yet) do you not understand?
• There was no part of this assignment that I did not understand because the instructions were straightforward.
4. Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not?
• I was initially unsure how the massive amounts produced by microarrays were analyzed but I now understand how this data can be organized efficiently.

James P. McDonald 21:02, 2 April 2013 (EDT)

## Helena M. Olivieri Week 9 Journal

1. What aspect of this assignment came most easily to you?
• The simple statistical analysis came the most easily.
2. What aspect of this assignment was the most challenging for you?
• If you don't keep the data organized and stay focused, it becomes very easy to make a simple mistake. So I suppose, staying engaged in the number "crunching" can be a little challenging.
3. What (yet) do you not understand?
• How we are going to analyze and compare our data when looking at more than one microarray data set.
4. Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not?
• So far, "crunching" the data has been a good hands on way to understand microarray experiments and data. But, the work is very tedious and after a while it becomes a little difficult not to become somewhat robotic.

Helena M. Olivieri 21:32, 2 April 2013 (EDT)

## Matthew E. Jurek Week 9

1. What aspect of this assignment came most easily to you?
• I found that the basic Excel functions came most easily to me. Taking averages and creating the basic formulas within Excel wasn't too difficult.
2. What aspect of this assignment was the most challenging for you?
• The hardest part was working with such a large spreadsheet. I've never worked with a sheet this large. It was easy to lose my place or mix up columns. Working with such a wide array of data was challenging at times.
3. What (yet) do you not understand?
• I'm not sure I did the Bonferroni correction properly. Following the correction, I had zero p values that were less then .05 across all time points. Based on the questions following the correction I feel that's wrong. I checked my work a few times and still found zero p values in that range. I understand what the correction is geared towards, but I'm not sure it worked properly on my spreadsheet.
4. Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not?
• It appears a majority of the experiment is "crunching" numbers on a spreadsheet. Seeing that I just did this crunching, I would say I've done a majority of the experiment. Since these experiments are so data intensive, I feel I have a better understanding.

## Salman Ahmad Week 9 Journal

1. What aspect of this assignment came most easily to you?
• It was pretty easy to follow along in class and do the parts of the assignment we went over.
2. What aspect of this assignment was the most challenging for you?
• It was hard to keep everything straight. I ended up getting a few strange results, so I had to go back and do it a few times before it ended up being correct.
3. What (yet) do you not understand?
• I don't understand the reasoning behind the Bonferroni correction. It seems like it is unlikely to have many p-values after doing the calculation.
4. Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not?
• Yes. I now realize that working out all of the numbers is how to actually interpret the results from a microarray. It is easier to see now how specific genes can be picked out from the other thousands of genes that we are looking at.

Salman Ahmad 00:28, 3 April 2013 (EDT)

## Elizabeth Polidan Week 9 Journal

1. What aspect of this assignment came most easily to you?
• The manipulations in Excel were easiest. I have used this software often.
2. What aspect of this assignment was the most challenging for you?
• Even though I was able to manipulate the data with ease, I am concerned about one of my answers. I found the gene with the smallest p-value is a gene whose function is unknown. I am not sure that was the intended gene.
3. What (yet) do you not understand?
• Other than what I did wrong, it's pretty straightforward.
4. Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not?
• I think it is the best way to really get to know what the process is all about. I do believe that the College of Science and Engineering should seriously consider some way of getting students familiar with more intricate manipulations in Excel, SPSS, etc. earlier in their academic career.

Elizabeth Polidan 01:41, 3 April 2013 (EDT)

## Paul Magnano Week 9 Journal

1. What aspect of this assignment came most easily to you?
• Manipulating the data was the easiest part, because of the straight forward directions. All that you had to do was enter the formulas correctly.
2. What aspect of this assignment was the most challenging for you?
• The sanity check was confusing simply because it seemed that my data manipulations were incorrect, but after checking my spreadsheet formulas and seeing they were correct, it made sense.
3. What (yet) do you not understand?
• Nothing I understood why we were doing everything since it was explained in class as we did the manipulations.
4. Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not?
• Yes, before it seemed very hard considering the entire genome is being analyzed (in this case over 6000 genes) but after seeing how the data is organized I can see that as long as it is done carefully the experiment would be relatively straightforward.

Paul Magnano 01:50, 3 April 2013 (EDT)

## Anthony J. Wavrin Week 9 Journal

1. What aspect of this assignment came most easily to you?
• The statistics portion, being involved in research for a few years has given me a lot of exposure to statistics and how it can be used, and misused, to show data. Thus, manipulating the p values and log changes to see how many genes had a large change in expression was a good example of going being the “significant” value.
2. What aspect of this assignment was the most challenging for you?
• The actual manipulation and sorting on the excel sheet. It was so much challenging as it was more grunt work that took time. I know that it is necessary but, it is not a very enjoying, nor stimulating activity.
3. What (yet) do you not understand?
• With regards to understanding DNA microarrays and statistics, I am fairly comfortable with those subjects. However, I have no idea how we are supposed to model all of this not just mathematically difficult but, the 6189 genes and trying to model all of them correctly is was I do not understand.
4. Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not?
• I think that it may have helped me understand it if I had never done anything like it before but, since I am in both of your classes and went to your lecture during convo, I felt like I had a very good grasp of the concept before this assignment.

Anthony J. Wavrin 02:32, 3 April 2013 (EDT)

## Ashley Rhoades Week

### Reflection

1. What aspect of this assignment came most easily to you?
• Looking through and reflecting on the data after sorting through it.
2. What aspect of this assignment was the most challenging for you?
• The most challenging aspect was keeping myself organized with all the columns of data.
3. What (yet) do you not understand?
• There is nothing I really don't understand, but I realize this is just the beginning of the project.
4. Does "crunching" the data yourself help you to understand microarray experiments better? Why or why not?
• For me it does help me understand the data better. I like statistics so this gave me an opportunity to look at the data through a familiar lens.

Ashley Rhoades 04:06, 3 April 2013 (EDT)