User: Christine Voellenkle

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9 years, 5 months ago
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9 years, 10 months ago
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Posts by Christine Voellenkle

<prev • 9 results • page 1 of 1 • next >
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dye swap control: discrepancy of correlation between R vs R and M vs M
... Dear BioC list, I am working with Exiqon miRNA arrays, performing 2-color labeling, comparing a cell line control versus cel line treatment I am trying to find a method to control for labeling bias. I read postings concerning this topic in the BioC archives, it says that the M values should be negat ...
mirna written 9.4 years ago by Christine Voellenkle90 • updated 9.4 years ago by Peder Worning100
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exclude spots with zero weight 0 from lmfit toptable list in limmaGUI
... Dear BioConductor mailing list! I perform 2 color hybridization with Exiqon slides, where each mir has 4 replicates. I compare a rather small number of slides (from 2 up to 6 biologial replicates for each treatment). For analysis of the data I am using the R-2.8, the limma package and its interface ...
normalization limma limmagui written 9.7 years ago by Christine Voellenkle90
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statistics for differential expression: adjusted p-values<0.05 BUT negative B-odds?
... Dear BioConductor mailing list! I am using the R-2.7.2, the limma package and its interface limmaGUI. I have a rather small number of slides (6) and probes spotted in 4 replicates (776x4=3104 spots). I perform background correction (normexp, cutoff=10), within (global loess) and between (Scale) arra ...
normalization limma limmagui written 9.8 years ago by Christine Voellenkle90 • updated 9.8 years ago by Paolo Innocenti320
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Comment: C: duplicate correlation of 4 "within array replicates" limmaGUI
... Dear Gordon, the spacing 1408 worked, perfectly!!! Thank you so much! Christine On Wed, Oct 15, 2008 at 3:34 AM, Gordon K Smyth wrote: > Dear Christine, > > If your arrays truly consist of four subarrays, with each subarray having > identical probes in the same arrangement, then the s ...
written 9.8 years ago by Christine Voellenkle90
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Answer: A: asMatrixWeights: weights of unexpected shape
... Dear Gordon, I tried it without inputting also the GAL file- and it worked, thank you so much!!! Grazie mille! Even if there shoudn't be a contradiction between gpr and gal information, bvecause I created the gpr using exactly this gal file. Greetings Christine On Wed, Oct 15, 2008 at 3:41 AM, Gord ...
written 9.8 years ago by Christine Voellenkle90
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duplicate correlation of 4 "within array replicates" limmaGUI
... Dear Gordon, excuse me the last mail, I wasn't aware of the fact hatbI sent it to you personally. Dear Gordon, thank you a lot for your fast answer! I attached a schema of the slide-design, also with an example of the 4 replicates, hoping that like this I could explain it sufficiently. For my under ...
limma written 9.8 years ago by Christine Voellenkle90 • updated 9.8 years ago by Philipp Pagel190
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Answer: A: duplicate correlation of 4 "within array replicates" limmaGUI
... Dear Gordon, Excuse me for the last mail, I simply replied, I didn't realise that I was sending it to your personal email. Thank you a lot for your fast answer! I attached a schema of the slide-design, also with an example of the 4 replicates, hoping that like this I could explain it sufficiently. ...
written 9.8 years ago by Christine Voellenkle90
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asMatrixWeights (weights, dim(M)), weigths of unexpected shape
... Dear Gordon, Excuse me for the last mail, I simply replied, I didn't realise that I was sending it to your personal email. I have also another problem with limma GUI- the Gene pix flag weighting. In my gpr file I have flag bad (-100), flag not found(-50) and unflagged (0), when I use spot quality w ...
gui limma written 9.8 years ago by Christine Voellenkle90
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duplicate correlation of 4 "within array replicates" limma gui
... Dear all, I perform 2 color hybridization, using microRNA and Exiqon slides. slide design: 4 replicates of 1 array each array consits of 8 subarrays, each subarray of 16 columns and 11 rows each mir has 4 replicates For analysis of the data ...
gui limma microrna written 9.9 years ago by Christine Voellenkle90

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