Hi everyone, I think i have problems when I import data in partek. I have mouse affy arrays. Lets say 4 diets in triplicates. I imported all data together with the RMA setting and did analysis for DEG and got nothing! Since i have very strong evidence from other experiments that it definitely has an effect I cant believe that there are no DEGs. So then I imported 1 diet at a time withRMA setting each time. Then I merged these together into one filr and checked for DEG. I got 1500 now. But I am not sure if I can rely on that. Strangely when i look back at the intensities for some genes these replicates have ditto value for e.g. If value is 6.3020 for a probe thrn it is 6.3020 in my other replicates of the same diet. How can the intensities be like this? Effect of RMA? Data imported wrongly? Thanks in advance!
0 answers
No answers yet.
Log in to answer this question.
-
Can I pool samples treated with different sgRNAs when testing for KO effects in RNA-seq analysis?
written by GLG •
-
How is the bootstrapping information from kallisto treated in DeSeq2 when imported using tximport?
written by divya.nandakumar •
-
Setting Up Model in DeSeq2
written by lkw222 •
-
lesser fold change value using RMA background correction
written by Paul
-
RNA-seq replicates not clustering
written by sckinta
-
Analysis with no Differentially Expressed Genes?
written by vitor.saldanha11 •
-
Is labeling important as a QC? I dont have any DEG across 8 diets which is really weird!
written by sshibin •
-
DESeq without replicate nbinomTest method
written by Bioblazer
-
Edited: RNA-Seq Analysis with EdgeR for Two-Way ANOVA: Am I doing this right?
written by ahhn •
-
RUVseq to correct for unwanted variance, interpreting p-value distribution
written by thomas.m.wolfe •
Your best bet is to contact Partek support. Since you are paying for a license may as well avail of that facility. They may be able to a GoToMyPC type session and work with you interactively, if this is your first time using Partek.
That said, if there are x samples in an experiment then they should all be imported in at the same time and processed as a set.