1 vote

Analysing the Effect of a Drug on the Morphological Changes of a Cell Type

Yes it's easy you load everything into a dataframe, so each variable is one column and perform supervised machine learning. That will solve all questions. Hypothesis 1 The target is 'pre' 'post' if ...
M__'s user avatar
  • 11.9k
1 vote

Heat map of protein expression from normalized abundance

The -2 to 2 should be the normalized version of log2 data (maybe mean or median normalization). This is commonly used in heatmaps to show downregulated value vs. upregulated value.
Pete Kittinun's user avatar
1 vote

Help with performing PCA analysis on data from 3 different datasets of normalized counts data for RNA-seq experiment

So I need to combine all the datasets to only compare the genes found in all the datasets mentioned and then perform a PCA analysis on those genes only. You can merge all your datasets for common ...
Nitesh Shriwash's user avatar
1 vote

Help with performing PCA analysis on data from 3 different datasets of normalized counts data for RNA-seq experiment

I think you are making this harder than you have to. Why can't you follow the code used in the vignette for making PCA plots? It doesn't even involve getting all the way to the DE genes.
swbarnes2's user avatar
  • 1,882
1 vote
Accepted

Combining read counts from three separate GEO studies

Yes, but there will be a batch effect. Not that I know if, you'll need to use sva or something along those lines to handle the batch effect. Crossing your fingers and hoping the batch effect is small ...
Devon Ryan's user avatar
  • 19.6k

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