User: wd

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wd30
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Germany
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8 months, 2 weeks ago
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4 years, 6 months ago
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Posts by wd

<prev • 27 results • page 1 of 3 • next >
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Comment: C: avereps with probes mapping to multiple genes (Agilent dual color microarray)
... I am aware that it is not realistic to distinguish between identically duplicated genes with our microarray design. However, my aim was not to be able to distinguish these genes in microarray experiments, but that I do not have to exclude the multi-mapping probes from my array analysis, and hence, w ...
written 8 months ago by wd30
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Comment: C: avereps with probes mapping to multiple genes (Agilent dual color microarray)
... Dear Gordon and James Thank you for your replies. A pity that a microarray version of Salmon/kallisto does not exist. Regarding Gordons scepticism for the annotation: I do want to let you know that identical (95-100%) duplicated protein coding genes do exist in the spider mite genome (you can fin ...
written 8 months ago by wd30
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Comment: C: avereps with probes mapping to multiple genes (Agilent dual color microarray)
... Thank you James for the proposed solution, but for some reason R always stops after running the third "mapper" line. I also do not completely understand the code. You make a factor of each ID in the SystematicName column, but then the use of mapper in the 4th and 5th line I do not understand... ...
written 8 months ago by wd30
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Comment: C: avereps with probes mapping to multiple genes (Agilent dual color microarray)
... Dear James My apologies for the confusion. I did not know that these were well-established human-IDs, but thaught these were random IDs. However, I do know the decision I want to make. I want to average/group probes, including multi-mapping ones, for each spider mite gene. I just could not figure ...
written 8 months ago by wd30
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Comment: C: avereps with probes mapping to multiple genes (Agilent dual color microarray)
... Dear James Thank you for your reply. However, I copied (and modified) the raw Agilent file example from another topic (see [here][1]). In my array design for a non-model arthropod species, all probes map to the CDS of a protein coding gene (and not to introns or snoRNAs). My apologies for the c ...
written 8 months ago by wd30
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Comment: C: avereps(): 'ProbeName' or 'SystematicName' for agilent one-channel microarray?
... Dear Gordon Thank you for your time, and reply. I now posted a new question on the Bioconductor form. You can find it here: here. ...
written 8 months ago by wd30
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avereps with probes mapping to multiple genes (Agilent dual color microarray)
... Hi I have a set of old Agilent microarray gene expression data   (e.g. GSE80337 ) and would like to reanalyze the results using an updated  annotation. (fyi, the orignal array design was done in such a way that each transcript had 2 to3 probes). I first mapped the array probes against the new anno ...
microarray limma agilent probe mapping avereps written 8 months ago by wd30 • updated 8 months ago by Gordon Smyth38k
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Comment: C: avereps(): 'ProbeName' or 'SystematicName' for agilent one-channel microarray?
... Dear Gordon I have a "similar" problem as Kevin. I would like to average (non-duplicate) probes/gene using the avereps function for a dual color Agilent array. However, I have probes that map to multiple genes (identically duplicated). In the case of Kevin it would look like this.   Row Col Contr ...
written 8 months ago by wd30
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Comment: C: DESEq2 comparison with two conditions and paired experiments
... Dear Prof. Love Thank you for your reply. I guess I'll have to perform more downstream experiments whether the DEGs of the ad-hoc procedure are meaningful. Just to give you an idea: this is a gene that is not significantly downregulated (based on FDR) according to the recommend test (test of inter ...
written 9 months ago by wd30
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Comment: C: DESEq2 comparison with two conditions and paired experiments
... Hi I have a similar setup of experiments (but with experiments not being paired) I have two genotypes (geno): "A","B", Two treatments (treat): "control" "damage" Four replicates for each genotype/treatment combination, 16 samples in total I want to know whether the effect of "damage" compared to ...
written 9 months ago by wd30

Latest awards to wd

Popular Question 8 months ago, created a question with more than 1,000 views. For differential expression analysis of htseq data with edgeR/voom
Popular Question 2.3 years ago, created a question with more than 1,000 views. For outlier detection of RNAseq samples
Popular Question 2.3 years ago, created a question with more than 1,000 views. For ape - delete bootstrap values (node.labels) less than a certain value

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