User: VeloSand

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VeloSand0
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Posts by VeloSand

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Comment: C: Should I use RUVseq on raw counts or on normalized counts coming from EDASeq pac
... Thanks a lot for your answer. You are right I'm expecting a lot of gene deregulations for some of the tested conditions. I tested both approach (RUVg on raw counts and RUVg after EDA UQ normalization. Even in this case, RUVg after EDA seems to work better (even though it is not perfect). ...
written 5 weeks ago by VeloSand0
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Should I use RUVseq on raw counts or on normalized counts coming from EDASeq package
... Hi, I'm working on an RNAseq experiment with spikes added and I would like to use RUVseq package. I had a look in the documentation and started with the very nice example on zebrafish. In this example RUVg is run on the object obtained after betweenLaneNormalization of the EDA package which is equiv ...
ruvseq written 5 weeks ago by VeloSand0 • updated 5 weeks ago by davide risso830
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xy2indices in Affy package : nr or nc parameter
... Hi, I'm having trouble when using the xy2indices function of affy package. In version 1.40.0 of affy, one parameter for this function was nr (number of rows on the chip). In the version I'm currently using 1.48.0 (but it was already the case in version 1.46.1), this parameter doesn't exist anymore ...
affy xy2indices written 4.0 years ago by VeloSand0 • updated 4.0 years ago by James W. MacDonald51k

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