JEFworks
commented
6 years ago Hi Marina,
Hum, yes it is currently a little confusing. scde.expression.difference compares the cells you specify in the groups factor and the up and down directions are set based on the order of the factor levels. Ideally, we can take levels(group) and concatenate it to column names or something.
But the direction is always the same! It is always the first level in the group factor compared to the second. So if you want genes upregulated in the second group, you will want to look for gene down regulated int he first group (since it is a pair-wise comparison). Or you can reset the levels of your group factor to be ordered the way you want.
You can differentiate between up vs. down-regulation by the MLE column (the maximum likelihood estimate of the expression-fold change).
Best, Jean
Jean Fan, PhD Bioinformatics and Integrative Genomics NCI F99/K00 Post-Doctoral Fellow Zhuang Lab | Harvard University 12 Oxford St, Naito 031, Cambridge, MA 02138 web: jef.workshttp://jefworks.com/
On Apr 20, 2018, at 11:08 AM, mvalenzuelav notifications@github.com<mailto:notifications@github.com> wrote:
Hi Jean, I just have one (I guess) simple question that I do not manage to understand. In the results file from scde.expression.difference, I can not see if up- and down-regulated genes come from one or the other group of cells. How can I know that? Is there any way to print in another column whom they are referred to? I am solving this by using scde.test.gene.expression.difference and selecting some of the most up- and down-regulated genes and examining plots from each group (the group with more expression is where this gene is up/down-regulated, I guess). But this is very annoying for almost 17000 genes and also it appears to me that always the first group I selected to create scde.error.models is the one that shows the down- or up-regulations. Is this meaning that the comparison is always going in the same direction? I mean, that the function is only returning changes in genes in one of the groups (first one) compared to the other (second), but not changes in the second group compared to the first one. Is this possible or is there any way to differenciate these changes (up/down-regulations)? Thanks very much in advance. Best, Marina
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mvalenzuelav
Hi Jean, I just have one (I guess) simple question that I do not manage to understand. In the results file from scde.expression.difference, I can not see if up- and down-regulated genes come from one or the other group of cells. How can I know that? Is there any way to print in another column whom they are referred to? I am solving this by using scde.test.gene.expression.difference and selecting some of the most up- and down-regulated genes and examining plots from each group (the group with more expression is where this gene is up/down-regulated, I guess). But this is very annoying for almost 17000 genes and also it appears to me that always the first group I selected to create scde.error.models is the one that shows the down- or up-regulations. Is this meaning that the comparison is always going in the same direction? I mean, that the function is only returning changes in genes in one of the groups (first one) compared to the other (second), but not changes in the second group compared to the first one. Is this possible or is there any way to differenciate these changes (up/down-regulations)? Thanks very much in advance. Best, Marina