User: j.baldauf
j.baldauf • 0
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Posts by j.baldauf
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... Hi Lluís, thanks for your reply. I saw that post, but I also wasn't successful building that package by myself.
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written 15 months ago by
j.baldauf • 0
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... Hi there,
I performed a consensus WGCNA analysis with two different Zea mays probes and identified 109 Modules. Next, I would like to perform a Go enrichment analysis using the function GOenrichmentAnalysis, but, it seems there is no org.Zm.eg.db available! Can anyone help me how to proceed? I am j ...
written 15 months ago by
j.baldauf • 0
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... Hi Jim,
I guess there is still no org.Zm.eg.db package available (I couldn't find one), therefore, I tried to build it by my self, like you described it. But I failed building and installing the package, could you please give me some hints how to do that? I was trying to use Devtools, but got the f ...
written 15 months ago by
j.baldauf • 0
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... Thanks for your response. If it is just an arithmetic rearrangement, shouldn't there be a "+" somewhere?
Irrespectively, my results show the same number of differentially expressed genes for both contrasts, so in total 203 genes show expression changes over development between the 2 genotypes.
But ...
written 2.3 years ago by
j.baldauf • 0
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... Hi again,
I have an RNA-seq experiment with samples of different genotypes and 3 different developmental stages. For each sample I determined a "genostage" factor
genotype <- rep(c("WT","Geno1","Geno2",<other genotypes>), each = 12)
dev <- rep(c("stage1","stage2", <other stages>) ...
written 2.3 years ago by
j.baldauf • 0
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... Hi again,
I was wondering, how I would define the contrast to determine changes in expression over time between two genotypes. According to examples in the limma manual, I would define the contrast like that:
(genostageG1_stageII-genostageG1_stageI)-(genostageG2_stageII-genostageG2_stageI)
But th ...
written 2.3 years ago by
j.baldauf • 0
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... when I include the blocking factor, I obtain different numbers of differentially expressed genes in comparison to not including the blocking factor? I merged the flowcell and lane factors as you suggested into one blocking factor.
genostageG1_stageI-genostageG2_stageI with blocking
-1 ...
written 2.3 years ago by
j.baldauf • 0
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... Thanks James and Aaron for your help and recommendations :)
To test weather there are any correlations between my samples processed on the same lane, how would I correctly define the blocking factor feeding to duplicateCorrelation?
What I tried is the following:
I defined in addition to the geno ...
written 2.3 years ago by
j.baldauf • 0
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... Dear all, I hope to get some elp in setting up my factors and the model matrix to determine differentially expressed genes.
I have a RNA-seq data set with samples of 13 genotypes and 3 developmental stages and of each sample, I have 4 biological replicates (in total 180 RNA-seq samples or columns i ...
written 2.3 years ago by
j.baldauf • 0
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Answer:
A: workflow.R in BioC 3.3
... I just observed the same error message. Do you already know when this problem will be fixed?
...
written 3.0 years ago by
j.baldauf • 0
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