Difference between revisions of "Kevin Wyllie Week 12"
From LMU BioDB 2015
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#* Only one GeneName column was used for this sheet (column A), as all of the columns had been confirmed to be identical between files. | #* Only one GeneName column was used for this sheet (column A), as all of the columns had been confirmed to be identical between files. | ||
#* The LogRatio data for each file was pasted into columns B through I, maintaining the previously mentioned file name headers. The data was pasted in the order of the file name numbers, from smallest to largest. | #* The LogRatio data for each file was pasted into columns B through I, maintaining the previously mentioned file name headers. The data was pasted in the order of the file name numbers, from smallest to largest. | ||
| − | # A new sheet was created, named " | + | #* '''Note: Rows not containing genes existing in the ''B. cenocepacia'' genome must be removed. In theory, this is very easy to do. Search results for examples of the several gene ID formats in burkholderia.com (set to ''Burkholderia cenocepacia'' J2314) suggest that the formats used are those that start with "BCAS," "BCAM," "BCAL" and "pBCA." However, we were not sure, logistically, how to apply a filter in Excel which would select for these gene ID's, primarily because you cannot apply two "Begins with" filters simultaneously (required to include the "pBCA" genes). |
| − | #* All content from the "genename_logratio" sheet was pasted into the " | + | # A new sheet was created, named "compiled_raw_data". |
| − | + | #* All content from the "genename_logratio" sheet was pasted into the "compiled_raw_data" sheet. | |
| − | + | ||
| − | + | ||
#* Finally, a new row was inserted under the header row. These row was titled "ExpName". The purpose of this row is to indicate what kind of cells were used for the corresponding experiment. Cells B2-F2 contain "Biofilm" as these columns correspond to experiments using biofilm cells that were ''not'' treated with tobramycin (125_1, 125_2, 125_3, 125_4, 126_1). Cells G2-I2 contained "Tobramycin" as these columns correspond to experiments using biofilm cells that were treated with tobramycin (126_2, 126_3, 126_4). | #* Finally, a new row was inserted under the header row. These row was titled "ExpName". The purpose of this row is to indicate what kind of cells were used for the corresponding experiment. Cells B2-F2 contain "Biofilm" as these columns correspond to experiments using biofilm cells that were ''not'' treated with tobramycin (125_1, 125_2, 125_3, 125_4, 126_1). Cells G2-I2 contained "Tobramycin" as these columns correspond to experiments using biofilm cells that were treated with tobramycin (126_2, 126_3, 126_4). | ||
Revision as of 03:07, 24 November 2015
Electronic Lab Notebook
Sample-Data Relationship:
Compiling Data
- From each raw individual data file, columns M ("GeneName") and R ("LogRatio") were copied and pasted into a new Excel file.
- All of the GeneName columns were pasted adjacently (columns A-H).
- Similarly, all LogRatio columns were pasted adjacently (columns I-P).
- To rule out the possibility of confusing any two files with each other, a header was added at the top of each column, with each corresponding file name for example (125_2, for example).
- The GeneName columns were scanned for any discrepancies n terms of amount of rows or ordering of gene ID's. The LogRatio columns were scanned for discrepancies in amount of rows.
- This sheet was named "allgenename_logratio".
- A new sheet was created, named "genename_logratio"
- Only one GeneName column was used for this sheet (column A), as all of the columns had been confirmed to be identical between files.
- The LogRatio data for each file was pasted into columns B through I, maintaining the previously mentioned file name headers. The data was pasted in the order of the file name numbers, from smallest to largest.
- Note: Rows not containing genes existing in the B. cenocepacia genome must be removed. In theory, this is very easy to do. Search results for examples of the several gene ID formats in burkholderia.com (set to Burkholderia cenocepacia J2314) suggest that the formats used are those that start with "BCAS," "BCAM," "BCAL" and "pBCA." However, we were not sure, logistically, how to apply a filter in Excel which would select for these gene ID's, primarily because you cannot apply two "Begins with" filters simultaneously (required to include the "pBCA" genes).
- A new sheet was created, named "compiled_raw_data".
- All content from the "genename_logratio" sheet was pasted into the "compiled_raw_data" sheet.
- Finally, a new row was inserted under the header row. These row was titled "ExpName". The purpose of this row is to indicate what kind of cells were used for the corresponding experiment. Cells B2-F2 contain "Biofilm" as these columns correspond to experiments using biofilm cells that were not treated with tobramycin (125_1, 125_2, 125_3, 125_4, 126_1). Cells G2-I2 contained "Tobramycin" as these columns correspond to experiments using biofilm cells that were treated with tobramycin (126_2, 126_3, 126_4).
To Do
- Begin statistical analysis.
- Upload spreadsheet.
- Add good-practice content/links.
