User: Juan C Oliveros Collazos

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Posts by Juan C Oliveros Collazos

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Answer: A: Background correction (Normexp+offset)
... Hi, You can even use offset = 0 to get more genes with higher fold changes but, many of them will have very low intensities, will not be biologically relevant and can be artifacts that introduce noise in the functional analysis. Unfortunately, using an offset or another will not solve the problem ...
written 8.4 years ago by Juan C Oliveros Collazos190
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Answer: A: Background correction (Normexp+offset)
... Hi Priyanka, I am pretty sure that the differences in the cases 1. 2. and 3. are due to low expressed genes. The offset can affect only the results for genes with very low intensities. I always use normexp and offset=50. Then, I look up the MA plot to decide which combination of Fold Change and p. ...
written 8.4 years ago by Juan C Oliveros Collazos190
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Answer: A: ExpressionSet without normalization
... Hi, the "rma" function of the "affy" package can be applied without normalizing the data. Use the option "normalize=FALSE". The same apply for the background correction ("background=FALSE") For more details check the function with, "?rma" in the R console. best, Juan Carlos On 07/07/2011 08: ...
written 8.4 years ago by Juan C Oliveros Collazos190
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Answer: A: mirna20.db
... Dear Ed, I had the same problem days ago. The file for miRNA2.0 exists but only for the most recent version of bioconductor (2.8) Try to update bioconductor (and maybe R) and check it again. best, Juan Carlos On 06/30/2011 12:20 AM, Ed Siefker wrote: > I am trying to annotate a project with ...
written 8.4 years ago by Juan C Oliveros Collazos190
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Agilent Feature Extraction Software vs GenePix Pro
... Dear all, In our group we are moving from GenePix Pro (scanner and sofware from Molecular Devices) to Microarray Feature Extraction Software (scanner and software from Agilent) to analyze two color arrays from Agilent. We use limma and Rank Products for detecting differential expression. In our ex ...
microarray limma written 9.0 years ago by Juan C Oliveros Collazos190
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Answer: A: simple functional analysis of gene lists
... (My apologies if this is not the proper place for introducing a non-R-based tool) Rainer. We developed a very simple tool for grouping genes in base on their annotations, that can be useful for you. You just need a list of gene names and their functional annotations (sentences in free t ...
written 9.7 years ago by Juan C Oliveros Collazos190
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Answer: A: How does the rank product calculate the fold change
... Dear Georg, Please check if your Fold Change values correspond to: FC = 2**logRatio (when logRatio >= 0) and FC = -2**.(-logRatio) (when logRatio < 0) logRatio is the difference of means assuming that the means are log(2) intensities. This is the usual way to defin ...
written 9.8 years ago by Juan C Oliveros Collazos190
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Comment: C: within array normalization for one color agilent array.??
... Dear Marc, There is a previous answer to another user with the same problem. Source: https://stat.ethz.ch/pipermail/bioconductor/2007-January/015532.html I paste the text here (original by Dr. Gordon K Smyth) ---8<-------------- The error message is telling you that there aren't enough rows ...
written 9.8 years ago by Juan C Oliveros Collazos190
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Comment: C: limma and Rank Products: comparison of the number of results
... Wolfgang, We apply this kind of methods just to find candidates to be confirmed experimentally in posterior analysis. We expect to have a percentage of false positives which is better for us than having false negatives. But with independence of the cutoff, we observed that --in this case-- Rank Pr ...
written 9.8 years ago by Juan C Oliveros Collazos190
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Comment: C: limma and Rank Products: comparison of the number of results
... Tom, Thanks for your message. Your explanations about the differences between the two methods are very clear and will help us to understand our results. Cheers, Juan Carlos Thomas Hampton wrote: > I have used rank products ad limma head to head many times, so I think > I understand your qu ...
written 9.8 years ago by Juan C Oliveros Collazos190

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