User: serpalma.v

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serpalma.v30
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Germany
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4 days, 11 hours ago
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2 years, 4 months ago
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Posts by serpalma.v

<prev • 27 results • page 1 of 3 • next >
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Should I contrast 2 treatment groups using the control group as reference or directly against each other?
... Dear community, I am analyzing RNAseq data set with DESeq2. Samples are grouped in three groups: one control group (n=16) and two case groups (case 1 and 2, n=6 and n=8, respectively). I want to find differentially expressed genes of both case groups against the control group, but also against eac ...
deseq2 contrast glm model.matrix written 6 weeks ago by serpalma.v30 • updated 6 weeks ago by Michael Love16k
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Comment: C: Multiple test corrections for planed contrasts
... The response says: If you control the FDR at a given level for each of 5 contrasts separately, then you have automatically controlled the FDR at the same level for all 5 contrasts together. I think is contradictory to what is writen in the DESeq2 Vignette (text cited in the initial post).  ...
written 10 weeks ago by serpalma.v30 • updated 10 weeks ago by Michael Love16k
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Multiple test corrections for planed contrasts
... I have a data set where samples are grouped according to their health status (3 levels) and sampling timepoints (2 levels for each sample). This would be a simplified version of the data set: df <- data.frame(status = c( rep("healthy", 4), rep("condition1", 4), rep("condition2", 4) ), ...
deseq2 contrast multiple comparisons written 10 weeks ago by serpalma.v30 • updated 10 weeks ago by James W. MacDonald45k
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Comment: C: Imputation method selection (mass spectrometry) bimodal distribution
... Thank you very much Laurent. I will go for the second method, as it is the one I can better understand how it works ...
written 12 weeks ago by serpalma.v30
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Imputation method selection (mass spectrometry) bimodal distribution
... I am currently processing a mass spectrometry data set with the Bioconductor package “Differential Enrichment analysis of Proteomics data” (DEP). The data set consists of 8 samples divided into two conditions, 4 animals per group. I followed the steps in the vignette of said package and I am at th ...
impute massspectrometry missing value imputation dep written 12 weeks ago by serpalma.v30 • updated 12 weeks ago by Laurent Gatto900
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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 16 months ago by serpalma.v30
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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 16 months ago by serpalma.v30
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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 23 months ago by serpalma.v30
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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 23 months ago by serpalma.v30
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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 23 months ago by serpalma.v30 • updated 23 months ago by Aaron Lun18k

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Scholar 2.1 years ago, created an answer that has been accepted. For A: Model matrix for anova in limma

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