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Nithisha
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@nithisha-14272
Last seen 6.1 years ago
Hi everyone,
I have some data from a Microarray experiment for 70 samples and they are for 3 different treatments across 5 timepoints (1h/2h/8h/24h/48h). This is how my data looks like; the number of samples I have for each Treatment for each time point.
| Time(hrs)/Treatment | Control | A | B | A+B |
| 1 | 3 | 2 | 3 | 4 |
| 2 | 3 | 3 | 3 | 3 |
| 8 | 3 | 3 | 4 | 3 |
| 24 | 5 | 5 | 5 | 5 |
| 48 | 4 | 3 | 3 | 3 |
I want to be able to compare upregulation and downregulation of genes between the 4 treatment groups at different time points.
In such a case, should I first create 2 columns in my metadata called Timepoint and Treatment Type first?
And how would I then create the design and contrast matrix? I appreciate any advice on this, thanks!
Hello Aaron,
Thank you so much for your reply. Section 9.5 of the user guide was very useful indeed. However, I am a little confused about what this means in the guide.
"A list of top genes for RNA2 versus RNA1 can be obtained from
> topTable(fit2, coef=1, adjust="BH") "Here, since sort.by is not specified, how is toptable ordering the results? (logFC/p value etc.)
Also, somehow my results for this seem to include the columns for my featureData together with the actual toptable output columns. If you would happen to know why, please do let me know.
Thank you for all your help!
Some basic R knowledge would be helpful here. If you look at
?topTable, you will see that the default value for thesort.byargument is"B", i.e., the function will return genes sorted by the B-statistic (also known as the log-odds). The same documentation will reveal that the columns offit$genesare added to the output table by default.Thank you, I shall look up ?topTable.