User: Stephen Rolfe

gravatar for Stephen Rolfe
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Posts by Stephen Rolfe

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Comment: C: Normalisation problem in metagenomeSeq
... On its way - thankyou! ...
written 3.6 years ago by Stephen Rolfe20
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Comment: C: Normalisation problem in metagenomeSeq
... Here's a link to the images http://imgur.com/Z2a5luv Sample 2 is 'good' , 3 is bad, but a plot of the raw counts for 2 vs 3 looks just fine ...
written 3.6 years ago by Stephen Rolfe20
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Normalisation problem in metagenomeSeq
... I have a problem with normalisation in metagenomeSeq and would appreciate some help. I have multifactorial data (root_type x genotype) and am looking for differential OTUs. I have created a biom table in Qiime and proceed as follows: bt=load_biom("otu_table_json.biom") pData(bt) #removing some c ...
normalization metagenomeseq written 3.6 years ago by Stephen Rolfe20 • updated 3.6 years ago by Joseph Nathaniel Paulson280
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Comment: C: oligo and pd.aragene.1.1.st annotation
... Thanks for the advice. I think my confusion arose probeset vs core in rma (and an interaction between oligo and affy). The affy files do contain AGI indices, gene symbols and descriptions and I've not yet got those into the analysis, but am trying the alternatives below. Cheers Steve On 07/08/201 ...
written 7.3 years ago by Stephen Rolfe20
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oligo and pd.aragene.1.1.st annotation
... I have a set of files from the new Aragene-1_1-st microarrays. I am using oligo to analyse these but have hit a problem with the annotation. I have the most up-to-date packages and don't hit any error messages. However, using getNetAffx doesn't seem to add annotation data to my rma normalised data ...
annotation limma category pdinfobuilder written 7.4 years ago by Stephen Rolfe20 • updated 7.4 years ago by Marc Carlson7.2k

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Popular Question 3.6 years ago, created a question with more than 1,000 views. For oligo and pd.aragene.1.1.st annotation

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