User: serpalma.v

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serpalma.v10
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Germany
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10 months, 2 weeks ago
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Posts by serpalma.v

<prev • 22 results • page 1 of 3 • next >
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Comment: C: matching probes to genes from pd.porgene.1.1.st array
... And which is your R version? I am working in windows 10 and also have installed Rtools 3.4   This is the output I get when trying to install the package and my session info: > install.packages("http://mbni.org/customcdf/20.0.0/entrezg.download/pd.porgene11st.ss.entrezg_20.0.0.tar.gz") Install ...
written 13 months ago by serpalma.v10
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Comment: C: matching probes to genes from pd.porgene.1.1.st array
... Wich R version are you working on? the package : install.packages("http://mbni.org/customcdf/20.0.0/entrezg.download/pd.porgene11st.ss.entrezg_20.0.0.tar.gz") It is not compatible with R 3.3.1, nor 3.2, nor 3.2.2     ...
written 13 months ago by serpalma.v10
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Comment: C: Does limma calculate pvalues using log2 fold changes or with linear values?
... Thank you very much Aaron, I normalized the array data with the RMA algorithm. According to this thread, RMA log transforms the data: https://support.bioconductor.org/p/50480/ ...
written 20 months ago by serpalma.v10
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Comment: C: Does limma calculate pvalues using log2 fold changes or with linear values?
... Dear Efstathios using the "linear" term was probably the wrong wording, I meant to say "not log scaled".  Best ...
written 20 months ago by serpalma.v10
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Does limma calculate pvalues using log2 fold changes or with linear values?
... Dear community, I am currently trying to figure out this question. I have tried different keywords but I do not seem to find the right thread.  What I want to know is: - Does limma arrives to a pvalue by using the log2 scale of the normalized array data? - Does limma arrives to a pvalue using th ...
limma log2 pvalue log2fc written 20 months ago by serpalma.v10 • updated 20 months ago by Aaron Lun17k
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Answer: A: Discrepancy in gene set size between gage() and geneData()
... Thanks Luo. I have checked the IDs in the "Gene" column of the table produced by geneData(). And as you said, some IDs are repeated. Once I apply unique(), I get the proper length.  One more thing. I see more genes in the set.size column than genes in the actual pathway. For example, I get for "ssc ...
written 21 months ago by serpalma.v10
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Discrepancy in gene set size between gage() and geneData()
... Dear community,  I have run GAGE and Pathview  on my microarray data. Everything worked fine. However, the number of genes assigned to a kegg pathway after using the gage() function is different from the number of genes produced by the geneData() function, which is the function to use in order to ...
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Low yield mapping ensembl transcript ids to entrez gene ids in biomart
... Hello everyone, I have a vector of 2906 ensembl transcript ids and I want to find their entrez gene ids using biomart, so I can do pathway analysis with gage. The problem is that using the code below, I only obtain 404 out of 2906. The ensemble transcript ids come from the annotations provided by ...
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Comment: C: Why are there so many not annotated probes in the PorGene-1_1-st affymetrix arra
... Thanks James, I was wondering now how to proceed with the pathway analysis.  There needs to be a set of regulated genes and a background in order to infer wether a pathway is enriched or not. For the background of genes I was thinking using all the annotated probes that belong to the "main" catego ...
written 22 months ago by serpalma.v10
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Why are there so many not annotated probes in the PorGene-1_1-st affymetrix array?
... Dear community, After creating an expression set for the PorGene-1_1-st affymetrix array. I found out that many of probes do not have annotations. As a result, once I am done with differential expression analysis, I found out many regulated probes that do not have any feature assigned assigned. The ...
annotation probe to gene id pathway analysis affymetrix microarrays pd.porgene.1.1.st written 22 months ago by serpalma.v10 • updated 22 months ago by James W. MacDonald45k

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Scholar 22 months ago, created an answer that has been accepted. For A: Model matrix for anova in limma

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