User: pbachali

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Posts by pbachali

<prev • 31 results • page 1 of 4 • next >
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Comment: C: Differential gene expression of longitudinal data
... Thank you Chris. I would try mixed models with repeated measures. ...
written 16 days ago by pbachali0
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Comment: C: Differential gene expression of longitudinal data
... The patients are paired samples. The patient were enrolled between 2009 to 2011. Basically the patients had follow up visits. For example the patientid 1 is same patient but quantitatively they are different because if you see the age parameter is different. And the reason was not mentioned why few ...
written 17 days ago by pbachali0
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Differential gene expression of longitudinal data
... Hi All, I am trying to perform differential gene expression of longitudinal data. In this longitudinal study 62 consecutive patients were enrolled and followed up prospectively. Age, disease activity were documented of all these patients in their each visit. The main challenge here is few patients ...
longitudinal data time course data written 18 days ago by pbachali0
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Comment: C: Regarding paired sample analysis (topTableF)
... Thanks for your insights and answers. Its very much clear. I am happy with the results I got. Now I have equal number of samples for each time-point.T0 (10), T12 weeks (10), T24 weeks(10). They are all paired samples. For instance say the number of samples vary each time point. Though they are paire ...
written 25 days ago by pbachali0
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Regarding paired sample analysis (topTableF)
... Hi, I am trying to find the DE genes between various contrasts using limma. My experimental design include 10 samples before immunosuppressive therapy and same 10 samples after 12 weeks of therapy and 24 weeks of therapy. I am trying to find the DE genes between various conditions like T12-T0, T24- ...
toptablef written 5 weeks ago by pbachali0 • updated 5 weeks ago by James W. MacDonald45k
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Filtering low intensity probes in microarray data
... Hi All, I have a question related to the analysis of the microarray data. In the process of differential gene expression analysis, filtering low probe intensities is very crucial. The array chip I am analyzing is HuGene1.0 ST array. I am using oligo package to analyze and rma normalization.  Can a ...
hugene1.0 st written 3 months ago by pbachali0 • updated 3 months ago by Gordon Smyth32k
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Comment: C: How to perform ANOVA to calculate differential gene expression with three catego
... My experimental design and the target table looks as follows: SUBJ.1720,SLE,baseline   baseline       Disease SUBJ.1720,SLE,week16    week16        Disease SUBJ.1720,week 52           week52        Disease I don't have any healthy samples to compare. I don't have any replicates either. All I hav ...
written 4 months ago by pbachali0
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Comment: C: How to perform ANOVA to calculate differential gene expression with three catego
... I have been using limma since two years. I have used ANOVA previously too but the problem was mainly with the traditional time course data. Because the data is longitudinal but they don't have any replicates. I was wondering how to do limma on this type of time course data. Anyways thanks  ...
written 4 months ago by pbachali0
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How to perform ANOVA to calculate differential gene expression with three categories
... Hi all, I have a good amount of experience in doing differential gene expression analysis in two categories like healthy samples and disease patients. Now I have three categories of patients at baseline, then at week 16 and week 52. I am thinking to try one way anova on this data. Any information o ...
anova written 5 months ago by pbachali0 • updated 5 months ago by Gordon Smyth32k
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Comment: C: Does GSVA enrichment score comes negative?
... Hi Robert, Thanks much. My apologies if I would have bothered you more regarding the GSVA.    Prat ...
written 6 months ago by pbachali0

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