User: lm795

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lm7950
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Posts by lm795

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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... Thanks for the extra advice. I am not familiar with that package so will have a look. I used BioMart before, as I can use that DB for orthologue mapping. I sometimes want to query Ingenuity Pathway Analysis DB (QIAGEN) and they only hold mouse and human data. Whenever I load fly gene IDs I get fairl ...
written 7 weeks ago by lm7950
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... Fair point James, I agree. I can always query BioMart to retrieve the extra annotation. Thanks again for your help! ...
written 7 weeks ago by lm7950
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... Thanks for the extra help James. The debugging process you suggested bypasses the error. I can finally move forward with my analysis and leave Partek Software behind ;) A few more points: 1. Is the reason for the failure in Benilton's approach the same as in the affycoretools, ie, the two da ...
written 7 weeks ago by lm7950
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... Many thanks James, I was trying the approach outlined initially (from a tutorial created by Benilton Carvalho) since the code you suggest above leads to an error message: > data.rma_V02 <- annotateEset(data.rma_V02, pd.drogene.1.1.st) Error: There appears to be a mismatch between the ...
written 7 weeks ago by lm7950
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... Many thanks James, I am obviously a novice. Unfortunately, all the features on the platform design (pd.drogene.1.1.st) return as "NA". Any thoughts for a plan B? > contrasts_30d[1:3,] coefficients.LL_30d...C_30d coefficients.LS_30d...C_30d coefficients.LS_30d...LL_30d df.residua ...
written 7 weeks ago by lm7950
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Applying NetAffx biological annotation to Affymetrix gene expression dataset
... I am running an analysis of transcriptional changes in Drosophila using Affymetrix (Drogene-1_1-st). The issue is that even though I can retrieve the biological annotation for the different probes, I do not know how to then merge the annotation with the primary data. How do I include the biological ...
microarray annotation written 7 weeks ago by lm7950 • updated 7 weeks ago by James W. MacDonald50k
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Problems with creating phyloseq bar plots from a table with species data
... I am trying to plot species abundance for intestinal bacteria analysed using a 16S RNA sequencing method. I am using RStudio (1.1.456) and R 3.5.1 My input is a file called "Species_percentages_test.csv", [here][1]. I was following the tutorial on "[Importing phyloseq Data][2]", more specifically, l ...
phyloseq microbiome analysis written 3 months ago by lm7950
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Exploring upstream regulators (transcription factors, drugs, etc) of transcripts in R
... I am interesting in identifying upstream regulators of a filtered group of transcripts, identified using either microarray or RNAseq technology. In the past, I have used Ingenuity Pathway Analysis (IPA) from QIAGEN. IPA's Comparison Analysis uses an Upstream Regulator analytic sub-routine. This pro ...
microarray bioconductor mapfromtranscripts cytoscape written 7 months ago by lm7950
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Comment: C: Getting R to talk to BioMart using biomaRt
... Many thanks Mike, the issue is now resolved. ...
written 7 months ago by lm7950
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Comment: C: Getting R to talk to BioMart using biomaRt
... Ok, I have Dropboxed gene_ids, with the header as a csv file here. Thanks again! ...
written 7 months ago by lm7950

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