User: ligia@ebi.ac.uk

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Last seen:
11 years, 9 months ago
Joined:
13 years, 3 months ago
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l****@ebi.ac.uk

Posts by ligia@ebi.ac.uk

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Comment: C: Help needed with configuration function from cellHTS2 package
... Hi Shripad, The problem is in your Plateconf.txt file: it has one extra (empty) column at the end of line 5. If you remove it (or use the attached file), it should work properly! Cheers, Ligia > Hello all, > > I am running an analysis of some cell assay experiments. I am getting an > ...
written 11.8 years ago by ligia@ebi.ac.uk50
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Answer: A: About subsampling of VST in lumi
... Hi Pan, Thanks for your email. The problem I reported is not due to the downsampling step controlled via "nSupport" parameter, but with a subsequent step in "vst" where if the number of selected probes with high variance (indSel) is above 5000, then only a random subset (5000) of these probes is us ...
written 11.8 years ago by ligia@ebi.ac.uk50
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Answer: A: Z factor and Z' factor
... Hi Steve, The difference is that the Z-factor assesses the screening assay quality using the distribution of the control values (either positive or negative controls, depending on the type of the assay) and the samples, while the Z'-factor is based exclusively on controls data using both positive a ...
written 11.9 years ago by ligia@ebi.ac.uk50
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Answer: A: Specifying wells in normalization for cellHTS2
... Hi Steve, You have to specify the negative controls in a way that is consistent with how they were annotated by the plate configuration file. The default annotation for negative and positive controls is "neg" and "pos", respectively, and such annotation is assumed by "normalizePlates" when you cho ...
written 11.9 years ago by ligia@ebi.ac.uk50
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Answer: A: Boxplots, different results?
... Hi, Jose I've also noticed this feature some time ago. It is related with the way they handle missing data. For example, if you save the output of boxplot in either case, we can see that: a = boxplot(MA$M[,1],MA$M[,2],MA$M[,3]) b = boxplot(MAw$M ~ col(MAw$M[,1:3])) the number of observations is d ...
written 13.3 years ago by ligia@ebi.ac.uk50

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