User: Erika Melissari

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Posts by Erika Melissari

<prev • 24 results • page 1 of 3 • next >
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Comment: C: interaction term contrast in Weaver mutant example of LIMMA manual
... Dear Jim, thank you for your always usefull explanations. If we observe a gene up-regulated in mutant "class" and also in the wt "class" but the extent of this up-regulation is different and statistically significant, we then should detect this gene as differentially expressed in this contrast...is ...
written 10.1 years ago by Erika Melissari240
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interaction term contrast in Weaver mutant example of LIMMA manual
... Dear bioconductor list, I am studing the Weaver experiment example of LIMMA manual and I am in a maze about the biological meaning of interaction term present among the contrasts. I did not manage to understend what kind of differentially expressed gene this contrast takes-out. The interaction cont ...
limma weaver written 10.1 years ago by Erika Melissari240 • updated 10.1 years ago by James W. MacDonald51k
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contrast matrix
... Dear Bioconductor list, I am performing a microarray data analysis of a reference design experiment. This is a part of the target file: Cy3 Cy5 M1775 Pool M1775 Pool M1775 Pool M1775 Pool M1775 Pool WT Pool WT Pool WT Pool WT Pool W ...
microarray limma written 10.2 years ago by Erika Melissari240 • updated 10.2 years ago by James W. MacDonald51k
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Answer: A: help needed on avereps function
... Dear Dr Pepin, thank you for your help. My sessionInfo() is: > sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 att ...
written 10.3 years ago by Erika Melissari240
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avereps function
... Dear list, I used averep function after normalization and before lmFit to average spot copies on microarrays. I noted that since a lot of spots have been averaged (the total number of spots have been reduced to 41000 from 43000), other spots do not have. See this example: Block Column Row ID ...
normalization written 10.4 years ago by Erika Melissari240
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Answer: A: avereps function
... Dear Claus-J?rgen, on avereps help I read: A new data object is computed in which each probe is represented by the average of its replicate spots. For an MAList object, the components M and A are both averaged in this way, as weights and any matrices found in object$other. For an MAList object, ID ...
written 10.5 years ago by Erika Melissari240
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Answer: A: avereps function
... Dear list, does anyone use avereps function by limma package to average probe copies on microarray? I used this function and obtained a strange result: my differentially expressed gene list sensibly change if I use or not this function (I perform the average before lmFit and after normalization). ...
written 10.5 years ago by Erika Melissari240
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avereps function
... Dear list, does anyone use avereps function by limma package to average probe copies on microarray? I used this function and obtained a strange result: my differentially expressed gene list sensibly change if I use or not this function (I perform the average before lmFit and after normalization). I ...
probe limma written 10.5 years ago by Erika Melissari240
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Answer: A: ...another question about using weights on microarray analysis
... Dear Matt, thank you for your help. My experimental design is a reference design with three classes and five array per class (a total of 15 arrays). We do not have technical replicates, but each array refers to a biological copy compared with a pool of the five wild type (we use dual-color microarr ...
written 10.7 years ago by Erika Melissari240
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...another question about using weights on microarray analysis
... Hello all, I have found discordant opinions among Bioconductor email regarding the use of quality weights on microarray analysis and I woul like to understand with clarity what to do before starting the statistical analysis of my last experiment. I use LIMMA to perform statistical analysis of micro ...
microarray limma assign written 10.7 years ago by Erika Melissari240

Latest awards to Erika Melissari

Popular Question 10.1 years ago, created a question with more than 1,000 views. For Use of duplicateCorrelation
Popular Question 10.1 years ago, created a question with more than 1,000 views. For avereps function

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