Katherine Grace Johnson Electronic Lab Notebook: Difference between revisions
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*Our transcription factors from deletion strains (CIN5, GLN3, HMO1, ZAP1) are not included on this list. | *Our transcription factors from deletion strains (CIN5, GLN3, HMO1, ZAP1) are not included on this list. | ||
*Use "Only DNA binding evidence" selection choice when generating networks in YEASTRACT |
Revision as of 15:46, 16 April 2015
This is my lab notebook
February 6, 2015
Repeat microchip data normalization for Ontario and GCAT from protocol Dahlquist:Microarray Data Processing in R. Data processed 1/30/15, but repeated today in order to record protocol to this notebook. Both normalized Excel data sheets will be compared to each other and to Natalie's to determine if there is a difference in normalization from computer to computer.
R x64 3.1.0 version used
Within Array Normalization for the Ontario Chips and Within Array Normalization for the GCAT Chips (includes between chip normalization)
- Change Directory - Must scroll down to "User" to locate kjohn102, then select folder "Microarray Data"
- to unzip files - right click, 7Zip, Extract here - this will place the unzipped file in the folder you are currently in
- R asks you to call the data file (.script), then an Excel target file (.csv) in which to put the normalized data. These must both be in the same folder (Microarray data), and downloaded before R is run
- Excel files are not generated until both normalizations are run
- Two Excel files generated: GCAT_and_Ontario_Within_Array_Normalization.csv and GCAT_and_Ontario_Final_Normalized_Data.csv. File desired is Normalized Data. Rename with suffix _date_GJ
- created Excel file, Comparison_Finalized_Normalized_Data_GJNW_20150206.csv to compare three sets of Normalized data: GJ1, GJ2, and NW
- GJ1 vs NW results - avg 10^-11 difference
- GJ1 vs GJ2 results - 0 difference
- Another normalization was run, named GJ3. This was compared to GJ2 in the Excel comparison document. Computer restarted, another normalization created - GJ4
- GJ2 vs GJ 3 results - 0 difference
- GJ3 vs GJ 4 results - 0 difference
Conclusions: Data normalization did not change from trial to trial on paradoxus computer, no matter the time of normalization. Normalization produced a slight difference between boulardii and paradoxus computers.
April 14, 2015
Completing Week 11 and Week 12 assignments from [BIOL398]. I will complete statistical testing of wild type data, and generate a network from this data.
Notes for improvement:
- use COUNTIF function instead of filtering the numbers when looking at p-values
- To prepare for analysis in STEM, columns containing #VALUE! had to be removed by using custom filter: does not equal #VALUE!. Remaining number values had to be copied and pasted into a new sheet.
- On macs, cluster files from STEM are not recognized by Excel. Textedit files must be converted to csv by the following procedure:
- Select a tab character and press Command F, Paste into top bar
- Click replace, then type a comma into the replace bar. Click replace all.
- Save with file extension .csv (type manually if it is not a drop down option)
YEASTRACT analysis of profile cluster #45
- 24 significant transcription factors
Sfp1p Fkh2p Yhp1p Yox1p Cyc8p YLR278C Ace2p Rif1p Msn2p Cse2p Stb5p Ndt80p Asg1p Msn4p Mig2p Snf2p Swi5p Spt20p Snf6p Pdr1p Gcr2p Gat3p Mcm1p Pop2p
- Our transcription factors from deletion strains (CIN5, GLN3, HMO1, ZAP1) are not included on this list.
- Use "Only DNA binding evidence" selection choice when generating networks in YEASTRACT