Notes from Kelsey:
The areas that your group worked on that I would like to finalize include:
1a EBSeq Can you verify that the full table is the only output we need for this. It was performed on the raw counts table, rather than normalized counts table. Is that okay?
2 Counts Normalization This is complete, but I only have access to my normalized counts table.
2a PCA Analysis You previously made PCAs that are separated for each cultivar. I would love 1 PCA for each time point that shows the distribution of cultivars and temperatures. I previously did this for the data, and it’s clear that there is primary variation based on cultivars and followed by temperature.
2b KEGG Analysis We got these output tables at 3 hours and 8 hours, but I know there are some loose ends we want to tie up with this. Can we get a list of the top KEGG pathways that are up- or down-expressed for each time point?
2b1 Pathview This will depend on the KEGG results
k-Means clustering This final addition has not been started, but it would be great to explore after our last meeting. Once we know how many clusters are present, we can investigate interesting ones that have genes regulated in a similar manner across the tolerant cultivars under heat stress.
Task
Major
Notes from Kelsey:
The areas that your group worked on that I would like to finalize include:
1a EBSeq Can you verify that the full table is the only output we need for this. It was performed on the raw counts table, rather than normalized counts table. Is that okay?
2 Counts Normalization This is complete, but I only have access to my normalized counts table.
2a PCA Analysis You previously made PCAs that are separated for each cultivar. I would love 1 PCA for each time point that shows the distribution of cultivars and temperatures. I previously did this for the data, and it’s clear that there is primary variation based on cultivars and followed by temperature.
2b KEGG Analysis We got these output tables at 3 hours and 8 hours, but I know there are some loose ends we want to tie up with this. Can we get a list of the top KEGG pathways that are up- or down-expressed for each time point?
2b1 Pathview This will depend on the KEGG results
k-Means clustering This final addition has not been started, but it would be great to explore after our last meeting. Once we know how many clusters are present, we can investigate interesting ones that have genes regulated in a similar manner across the tolerant cultivars under heat stress.