User: pbachali

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pbachali0
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Posts by pbachali

<prev • 35 results • page 1 of 4 • next >
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Pipeline for Lexogen Quantseq 3' UTR Sequencing
... I am trying to analyze the RNA Seq samples that were sequenced using Lexogen QuantSeq 3"UTR platform with NextSeq sequences. I was wondering if we could use the same tools we use to analyze the traditional RNA Seq experiment using HiSeq Sequencer. When I say tools, they are FastQC, trimmomatic, STAR ...
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Comment: C: Does GSVA enrichment score comes negative?
... Hi Robert, Firstly my apologies for posting it incorrectly. I thought I would follow the same thread since it is all about GSVA. I would post it correctly next time. Since I have started already here, I am using "ADD REPLY" for now. But from next time I will make sure I am posting the question corr ...
written 7 months ago by pbachali0
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Comment: C: Does GSVA enrichment score comes negative?
... Hi Robert, I have been using GSVA extensively for pathway centric analysis to understand the heterogenous populations and understand the pathways in each patient. This is quite a powerful program. I have a small question. It might be a simple one. As explained in the paper the input for the gsva is ...
written 7 months ago by pbachali0
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Comment: C: annotation for Agilent Mouse an d Human 8x60K array
... Hi All, I am not sure if this is the right place to post this question or not. Since my question is also related to Agilent human microarray annotations, I am trying to follow the same thread. Please feel free to delete the post if this is not relevant here. I am trying to find the annotation packa ...
written 9 months ago by pbachali0
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Comment: C: Differential gene expression of longitudinal data
... Thank you Chris. I would try mixed models with repeated measures. ...
written 11 months 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 11 months 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 11 months 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 11 months 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 12 months ago by pbachali0 • updated 12 months ago by James W. MacDonald48k
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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 14 months ago by pbachali0 • updated 14 months ago by Gordon Smyth35k

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Popular Question 5 months ago, created a question with more than 1,000 views. For Creating custom geneset
Popular Question 15 months ago, created a question with more than 1,000 views. For Creating custom geneset

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