Difference between revisions of "Asandle1 Week 9"
(→Electronic Notebook: added more) |
(→Electronic Notebook: added the p value checks) |
||
| Line 74: | Line 74: | ||
36) Saved to upload to the wiki. | 36) Saved to upload to the wiki. | ||
| + | 37) Uploaded to Wiki with same file name. | ||
| + | 38) Continuing, now with the "Sanity Check". | ||
| + | 39) Following the instruction and opening the dGLN3_ANOVA worksheet. | ||
| + | 40) Did the Data Ribon > Filter. This is a shortcut to autofilter instead of using the top bars. | ||
| + | |||
| + | 41) Expanded all the column headers so that they wouldn't be cut off by selecting all of them and double clicking between the column letter markers. | ||
| + | |||
| + | 42) Clicked on the dropdown for the unadjusted p-value. | ||
| + | |||
| + | 43) I selected a criterion to only show p-values less than to 0.05. There are 2531 genes with a p < 0.05. | ||
| + | |||
| + | 44) I repeated the process of checking criterion but for 0.01, 0.001, and 0.0001. The results were: | ||
| + | |||
| + | 1204 at 0.01, 514 at 0.001, 180 at 0.0001 | ||
[[Media:AS&CK_BIOL367_S24_microarray-data_dGLN3.xlsx]] | [[Media:AS&CK_BIOL367_S24_microarray-data_dGLN3.xlsx]] | ||
Revision as of 16:04, 20 March 2024
Contents
Electronic Notebook
1) Downloaded the gln3 data
2) Opened in Excel
3) Enabled Editing
4) Saved File with AS&CK_ before the rest of its name
5) Add a new sheet called ANOVA_dGLN3
6) Copied the Data from the Master_Sheet_dGLN3 to the new ANOVA_dGLN3
7) Created columns for Average Log called dGLN3_AvgLogFC_t for each time period adding 15,30,60,90, and 120 at the end.
8) Then we computed the average for the first row of t 15 time points of 2 through 5.
9) We copied down the formula all the rows
10)We noticed a DIV/0 Error for some rows since the data was blank.
11)Repeated the same process for the rest.
12)Creating a column for dGLN3_ss_HO for the sum of squares.
13) Highlighted the columns for all times for this and did =sumsq(all relevant data in the row)
14) Created Columns for dGLN3_ss_t15 through t120
15) Did the same process highlight the data in a row that applied to the specific time t.
16) Double clicked to expand
17) Was not the correct equation so deleted everything in the sumsq= that we just did except for the dGLN_ss_HO which was still correct
18) Instead we do number 14 in the worksheet.
19) For dGLN_ss_t15 the equation was =SUMSQ(D2:G2)-COUNTA(D2:G2)*X2^2
20) After completed copied down all the columns.
21) Created dGLN3_SS_full to the right.
22) Created the dGLN_Fstat to the
23) Took a weekend break
24) Back to the task
25) Added =SUM of the ss rows for the dGLN_SS_full
26) Double Clicked to Drop down for all of them
27) Counted my n for the fstat to be 20.
28) There was an error in my SS_Full, I should have only included the time times t15-120 and I accidentally included HO, removed it and the problem was fixed.
29) Now adding the Bonferroni and p value corrections
30) Created a box called dGLN3_Bonferroni_p-value and in the cell did = and selected AK2. Then did *6189.
31) Double clicked to fill the column.
32) Created a new column, dGLN3_Bonferroni_p-value correction. Entered =if(AL2>1,1,AL2) and then double clicked to expand down the formula.
33) Added a new worksheet to begin the Benjamini & Hochberg p value correction
34) Named worksheet dGLN3_ANOVA_B-H
35)Followed the Calculate the rest of the Benjamini & Hochberg p value correction section exactly.
36) Saved to upload to the wiki.
37) Uploaded to Wiki with same file name.
38) Continuing, now with the "Sanity Check".
39) Following the instruction and opening the dGLN3_ANOVA worksheet.
40) Did the Data Ribon > Filter. This is a shortcut to autofilter instead of using the top bars.
41) Expanded all the column headers so that they wouldn't be cut off by selecting all of them and double clicking between the column letter markers.
42) Clicked on the dropdown for the unadjusted p-value.
43) I selected a criterion to only show p-values less than to 0.05. There are 2531 genes with a p < 0.05.
44) I repeated the process of checking criterion but for 0.01, 0.001, and 0.0001. The results were:
1204 at 0.01, 514 at 0.001, 180 at 0.0001
Media:AS&CK_BIOL367_S24_microarray-data_dGLN3.xlsx
To User Page: User: Asandle1
To Template: Template:Asandle1
