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Day 14

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Haries Ramdhani edited this page Feb 13, 2017 · 3 revisions

Day 14 - February 6, 2017

Today I mostly worked with what I have been working on since Sunday. Continued writing the Dirty Codes.

For the purpose of reproducing the study (the first one is Distrubution of Log Fold Change) I use Python, because Python has IPython Notebook thus it will be easier to present the results of the analysis. The analysis can also be done in R (actually the author of the study mostly did the analysis in R).

There are several modules that I use for the analysis (I explained it in the notebook). What I did in the first notebook is:

  • Created the distribution of the log2 fold changes for both the RNA-seq and MS3 proteomics data
  • Calculated the number of the up regulated and down regulated genes for each data
  • Analyzed the intersection of the log2 fold changes distribution between the MS3 Proteomics and RNA-Seq data
  • Generated the venn diagram to see the genes that are found in both of RNA-seq and MS3 proteomics data set
  • Analyzed the genes with significant p-value and top ten genes with the highest p-value and with the highest fold changes
  • Compare the fold changes value between the intersection of the RNA-seq and MS3 proteomics data set.

Today I also tried to learn how to generate heatmaps using python-seaborn. Took a look at the TOPGo and how can we visualize the results (which then I found that we cannot use TOPGo to visualize the data but we can use other R libraries). Here are some of the things that I learned today:

  • How to perform gene ontology gsea using Panther. (I also tried to find the programmatic access way to Panther but couldn't find one)
  • I also found this thing called Homer which is also a tool for functional enrichment analysis for microarray data but I didn't use it
  • Because it's been a long time since the last time I used python-seaborn and other libraries that I used to perform the analysis, I mostly visited Stackoverflow to find the questions that are related with the problem that I experienced
  • I also found about Python's GSEA library but hadn't tried it yet
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