User: elisa.micarelli

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Posts by elisa.micarelli

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Answer: A: Connectivity Map: how are probe sets ordered for an instance?
... Hi, No, but I reprocessed the data according to this tutorial http://girke.bioinformatics.ucr.edu/longevityTools/mydoc/mydoc_longevityTools_eDRUG_04.html ...
written 10 days ago by elisa.micarelli0
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PubChem CID identifier
... Hi, I apologize in advance if I will be not enough precise in the question but I'm new in this field. I'm trying to perform a mapping between different compound identifiers by mean of PubChem database. I analyzed the compound identifiers such as PubChem CID, SID, InChI, SMILE and CAS number, more ...
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Connectivity Map: how are probe sets ordered for an instance?
... Hi, I'm studying the Connectivity Map data and I'm wondering how probe sets are ordered for an instance. I read the following paragraph in help section of Connectivity Map (https://www.broadinstitute.org/cmap/help_topics_frames.jsp): "[..] All average difference values from the treatment scan are ...
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Microarray Data Processing
... Hi, I'm trying to study and understand how the MAS 5.0 algorithm works. I'm reading this manual http://media.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf. This is the first time that I approach this field and the steps for processing the data are enough difficult and often uncl ...
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Comment: C: Perturbation scan id in Connectivity Map data
... Thanks for the answer. Yes indeed these instances are biological replicates, I was perplexed just about the "slight" difference between lists of probe set positions, but this is the reproducibility. Thanks again. ...
written 16 months ago by elisa.micarelli0
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Perturbation scan id in Connectivity Map data
... Hi, I'm studying the connectivity map approaches and data. Looking at the instances table I noted that there are some instances related to the same drug in same cell type, at same concentration and duration, while the perturbation scan id and the instance id attributes change. My question is, how s ...
affymetrix array plate cmap written 16 months ago by elisa.micarelli0 • updated 16 months ago by Zhilong Jia1.1k
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Comment: C: Limma package: explanation makeContrasts examples
... I'm sorry, I wanted comment your answer but I was mistaken. However, I understood that for my analysis is necessary an anova analysis. So, thanks a lot for your advices and answers, now I'm going to read better the manual and understand the analysis that I should do. If I had any possible questions ...
written 2.2 years ago by elisa.micarelli0
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Comment: A: Limma package: explanation makeContrasts examples
... Thank for the answer. I don't understand when should I specify the argument contrast in makeContrasts? Maybe I didn't unterstand the meaning of contrats. 2) the output in last part is the same, but in one case the makeContrasts returns (near Levels) the word contrast in the other one returns the s ...
written 2.2 years ago by elisa.micarelli0
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Limma package: explanation makeContrasts examples
... Hi, even at this stage, I want to thank anyone will can help me. I'm using the Limma package in order to anlayse the gene expression in different tissues(Sample). For each tissue I want to know which genes are overexpressed and underexpressed; for example I would be able to say that the gene_x is ...
gene R written 2.2 years ago by elisa.micarelli0

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For Limma package: explanation makeContrasts examples

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