http://vrl.cs.brown.edu/wiki/index.php?action=history&feed=atom&title=Daniela_Cipolletta 2026-04-20T22:01:40Z Revision history for this page on the wiki MediaWiki 1.43.1 http://vrl.cs.brown.edu/wiki/index.php?title=Daniela_Cipolletta&diff=5978&oldid=prev 2012-05-30T17:44:12Z

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Caroline Ziemkiewicz http://vrl.cs.brown.edu/wiki/index.php?title=Daniela_Cipolletta&diff=5977&oldid=prev 2012-05-30T17:41:25Z

<p>Created page with &quot;Intro This is new data that she hasn&#039;t looked at before, part of her current research project Comparing t-cells from different tissue (adipose tissue) Comparing in a differen...&quot;</p> <p><b>New page</b></p><div>Intro<br /> <br /> This is new data that she hasn&#039;t looked at before, part of her current research project<br /> Comparing t-cells from different tissue (adipose tissue)<br /> Comparing in a different mouse strain (from earlier experiments in this project<br /> <br /> Analysis<br /> <br /> - loading data into multiplot<br /> - opening a blank ppt presentation<br /> - names the slide<br /> - waiting on upload<br /> - starts setting up axes of a graph (on ppt), makes two graph setups, draws more labels<br /> - getting her slide set up while she waits on upload<br /> - has a side-by-side multiplot view<br /> - loads up each graph<br /> - turns graphs gray (familiar with graph design?)<br /> - selects some outliers, looks at sidebar table<br /> - changes graph 1, selects outliers again<br /> - saves the result<br /> - seems frustrated?<br /> - generating and saving graphs frequently<br /> <br /> ? she&#039;s highlighting with a previously discovered signature that she doesn&#039;t expect to be present here<br /> <br /> - adding lots of highlights<br /> - propagates highlights to view 2<br /> - looking at outliers<br /> - removing genes based on some criteria<br /> - highlighting several specific genes<br /> <br /> ? highlighting the transcription factors - hallmark genes of this (?) <br /> variance between knockout and wild type mice<br /> <br /> - generates a volcano plot (p-values)<br /> - propagates highlight, looks intently back and forth between the two<br /> - filters<br /> - looks at significant genes<br /> <br /> keeps needing to resize the window to change the settings and get back to a big view<br /> doesn&#039;t always use the multiple views in a linked fashion<br /> <br /> - nods to herself<br /> ? comparing FAT vs. something else<br /> wild type model significantly more represented<br /> strange bias toward wild type <br /> signatures that are either over-represented (red) or under-represented (blue)<br /> daniela reaches conclusion: knockout can move signature in this direction<br /> new information, but in line with previous observations<br /> <br /> - nods again<br /> looking at where stuff is... fitting expectations, etc.<br /> <br /> - propagates highlight again<br /> mostly seems to be doing manual linking<br /> <br /> - goes to get a colleague for discussion<br /> (videos break, sound probably goes slightly off-sync...)<br /> - returns<br /> - clears some highlights<br /> <br /> looking for a signature given by jaime. from another platform, so it needs to be translated.<br /> <br /> - finally finds the signature and puts it in her graphs<br /> - has trouble seeing what highlights are on due to screen space issues<br /> - puts highlight in view 2 and looks back and forth.<br /> <br /> Post-analysis discussion <br /> <br /> mice with transcription factor<br /> fusion with protein allowed genes to behave properly. <br /> looking if cells with these hallmark factors are different<br /> checked first replicate a month ago<br /> this is a follow-up experiment<br /> <br /> process steps:<br /> what is the variability?<br /> filter for most solid data <br /> looking from genes to see how they change<br /> <br /> previously, some genes don&#039;t belong to this, appearing in knockout mice <br /> check if there are still weird genes and find them<br /> <br /> next, to make a gene list of differnt experiments between animal models, study to see if they follow in a particular pattern.<br /> explain phenotype in disease?<br /> <br /> likes to have two plots to see two different comparisions for same population<br /> see significance as well as behavior<br /> if I don&#039;t have 2 I have to go back and forth<br /> 4 is even better <br /> sometimes you do multiple comparison - many populations<br /> going back and forth you can forget and lose time<br /> <br /> big files, 100 samples, 30 populations<br /> wants to grab multiple highlight files</div>

Caroline Ziemkiewicz