Difference between revisions of "Kzebrows Week 12"
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| + | ==Electronic Lab Notebook== | ||
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| + | First, I accessed the microarray data from [[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32978/files/ ArrayExpress]] and downloaded the files labeled "E-GEOD-32978.sdrf.txt" and "E-GEOD-32978.raw.1.zip" | ||
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| + | First we analyzed the data by opening the sdrf.txt file. From examining this file it was apparent that no dye swaps had occurred. We looked at the Comment [Sample_Title] column compared to the Label and FactorValue[TREATMENT] columns and found that each sample/control combo was repeated three times leading to a total of 72 samples, but each control was labeled with Cy3 dye and each treated sample was labeled with Cy5 dye. This was the extent of samples that occurred, which is improper technique, because the dyes have different affinities. This could potentially skew the results but we moved forward with our analysis. | ||
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| + | Next, I unzipped the raw data file, which expanded to 36 files. Each file contains a treatment and a control hybridized. We eliminated extraneous columns, leaving behind only Column E ("ID") and Column AS ("Log Ratio 635/535"). Because each file has columns with these titles, Column E was re-labeled " | ||
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| + | ==Class Notes 11/19== | ||
| + | *Open "raw" data file as .gpr in Excel | ||
| + | *Open "sdrf.txt" file in Excel | ||
| + | *Use Column E "ID" | ||
| + | *Use Column AS "Log Ratio 635/535" | ||
| + | |||
| + | |||
{{Template : Kzebrows}} | {{Template : Kzebrows}} | ||
[[Category : Journal] | [[Category : Journal] | ||
Revision as of 00:02, 20 November 2015
Contents
Electronic Lab Notebook
First, I accessed the microarray data from [ArrayExpress] and downloaded the files labeled "E-GEOD-32978.sdrf.txt" and "E-GEOD-32978.raw.1.zip"
First we analyzed the data by opening the sdrf.txt file. From examining this file it was apparent that no dye swaps had occurred. We looked at the Comment [Sample_Title] column compared to the Label and FactorValue[TREATMENT] columns and found that each sample/control combo was repeated three times leading to a total of 72 samples, but each control was labeled with Cy3 dye and each treated sample was labeled with Cy5 dye. This was the extent of samples that occurred, which is improper technique, because the dyes have different affinities. This could potentially skew the results but we moved forward with our analysis.
Next, I unzipped the raw data file, which expanded to 36 files. Each file contains a treatment and a control hybridized. We eliminated extraneous columns, leaving behind only Column E ("ID") and Column AS ("Log Ratio 635/535"). Because each file has columns with these titles, Column E was re-labeled "
Class Notes 11/19
- Open "raw" data file as .gpr in Excel
- Open "sdrf.txt" file in Excel
- Use Column E "ID"
- Use Column AS "Log Ratio 635/535"
Assignments
Individual Journal Assignment Pages
- Week 1
- Week 2
- Week 3
- Week 4
- Week 5
- Week 6
- Week 7
- Week 8
- Week 9
- Week 10
- Week 11
- Week 12
- Week 14
- Week 15
Individual Journal Assignments
- Kzebrows Week 1
- Kzebrows Week 2
- Kzebrows Week 3
- Kzebrows Week 4
- Kzebrows Week 5
- Kzebrows Week 6
- Kzebrows Week 7
- Kzebrows Week 8
- Kzebrows Week 9
- Kzebrows Week 10
- Kzebrows Week 11
- Kzebrows Week 12
- Kzebrows Week 14
- Kzebrows Week 15
- Final Individual Reflection
- Class Journal Week 1
- Class Journal Week 2
- Class Journal Week 3
- Class Journal Week 4
- Class Journal Week 5
- Class Journal Week 6
- Class Journal Week 7
- Class Journal Week 8
- Class Journal Week 9
- Oregon Trail Survivors Week 10
- Oregon Trail Survivors Week 11
- Oregon Trail Survivors Week 12
- Oregon Trail Survivors Week 14
Additional Links
- User Page: Kristin Zebrowski
- Class Page: BIOL/CMSI 367-01
- Team Page: Oregon Trail Survivors
[[Category : Journal]
