User: michel655

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michel6550
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Posts by michel655

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Comment: C: Microarray expression analysis for on factor taking account confounders (covaria
... Hello, oh great. i was trying to coerce instead of use my dataframe directely. So thanks for all your disponibility Aaron. ...
written 6 months ago by michel6550
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Comment: C: Microarray expression analysis for on factor taking account confounders (covaria
... Hello Aaron, I was waitng for more gene that's why i was thought my codes was wrong. So, i keep this result.Thanks for helping me. I have another issue in my limma analysis. I want to know how to transfrom a dataframe to a Elist object of limma package in order to perform the same analysis the one ...
written 6 months ago by michel6550
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Comment: C: Microarray expression analysis for on factor taking account confounders (covaria
... Hello Aaron, "All negatives" and "all positives" refer to non-significant and significant genes. This is my code : show (target) FileName PHENO SEXE AGE LEUC NP15014.txt 1 1 1 1 NP15016.txt 1 0 1 0 TA15052.txt 1 1 0 1 HPIKNP01.txt 1 1 0 0 NP1 ...
written 6 months ago by michel6550
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Comment: C: Microarray expression analysis for on factor taking account confounders (covaria
... Hello SamGG, for gene anaova statistics, i'm sorry i forgot to mention that Pvalue obtain with the logiciel are use to calculate the limite Pvalue for different FDR. So, our DEGs in GeneAnova are filtered according to FDR 10%. ...
written 6 months ago by michel6550
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Comment: C: Microarray expression analysis for on factor taking account confounders (covaria
... Hello Aaron, When i said "Any gene is upregulated" means "no gene is upregulated". Sorry. I perform the two approches you suggest me but it still seem that something wrong on my data and, by consequence, don't permit Limma to perform good statistics because my results are all negative in the first ...
written 6 months ago by michel6550
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Comment: C: Microarray expression analysis for on factor taking account confounders (covaria
... Hello Aaron, as I said to SamGG, i changed my lomumn name and put "PHENO" instead of "PHENOMM" in my matrix. I was trying to explain that any gene is upragulated with my topTable statistics up to 10% FDR. Anova test was perform not in R but with another tools called GeneAnova. The fact is either li ...
written 6 months ago by michel6550
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Comment: C: Microarray expression analysis for on factor taking account confounders (covaria
... Hello SamGG, I changed the columns names, so "PHENOMM" is called just "PHENO" on my matrix (to recover the initial name on the targets table).   ...
written 6 months ago by michel6550
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Comment: C: Microarray expression analysis for on factor taking account confounders (covaria
... Hello Aaron, thanks for your reply. I was confused bay the fact that this formula "model.matrix( ~PHENO+SEXE+AGE+LEUC)" gives me a matrix with 4 coefficenients corresponding to the 4 variables a put in formula and nothing with interaction terms like PHENO:SEXE and so on. That's why i was tinking th ...
written 6 months ago by michel6550
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Comment: A: Microarray expression analysis for on factor taking account confounders (covaria
... Hello SamGG, I have already perform a formula with + instead of * but it gives me only effect on each factors. It is not what i'm looking for. But thanks for your reply. ...
written 7 months ago by michel6550
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Microarray expression analysis for on factor taking account confounders (covariables)
... Hello everyone. I have a little question about how to design a matrix taking into account covariables. Subject : I have got agilent microarray data from 12 samples (6 mild malaria sample noted "MM" and 6 cerebral malaria noted "CM"). Data relative to age, sexe, ethnie and leucocytes count are also ...
limma design matrix matrix with covariables written 7 months ago by michel6550 • updated 7 months ago by Aaron Lun21k

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