User: ciemanek

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ciemanek110
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The Netherlands/Amsterdam
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ciemanek
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7 months ago
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Posts by ciemanek

<prev • 32 results • page 1 of 4 • next >
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Comment: C: How to acknowledge in the paper a reference genome that hasn't been published ye
... There is no paper regarding this particular genome and it is not available for download to the best of my knowledge. It was assembled by people I collaborate with, but as far as I understood their idea is to publish it in another paper in some time. The only information I have is that it was assembl ...
written 7 months ago by ciemanek110
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Forum: How to acknowledge in the paper a reference genome that hasn't been published yet?
... My question is a less technical one, but I was not sure where to seek advice. I am currently working on a paper regarding variants called from DNA-seq, but the reference genome that was used for calling variants hasn't been published yet (I mean the whole pipeline for assembling scaffolds and annota ...
paper forum reference written 7 months ago by ciemanek110 • updated 6 months ago by kate.kross900
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Answer: A: Hypergeometric test's summary error while using GOstats
... Hi Mario! Thanks a lot for your answer. In my case the problem was that my R version was not up to date. The latest topGO works perfectly fine with the newest R version (3.5.0) however at the time when I was perfofming my analysis R 3.5.0 was only available for Windows so I had to switch to my pers ...
written 9 months ago by ciemanek110
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Hypergeometric test's summary error while using GOstats
... Hi! I am trying to perform hypergeometric test to find enriched GO terms among the genes that differ significantly between two clusters. However, I have a problem when I try to get a summary of the hypergeometric test from GOstats package - I get the following error: > Error in initialize(value, ...
enrichment gostats go microarray written 10 months ago by ciemanek110 • updated 8 months ago by Dunja10
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Comment: C: Categorize patients based on continuous variables
... About the tissue specificity - the data I have is only tumor data, we have no controls for that and what I mean is that some of the genes might be co-expressed due to the tissue of origin. I wonder how I could account for that - should I look for control data in databases (problem is that sample siz ...
written 12 months ago by ciemanek110
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Comment: A: Categorize patients based on continuous variables
... Thanks a lot! I will definitely take a look into that - in general those sigantures mean expression is correlated with the level of differentiation and what is of interest to me is what are possible underlying differences between highly and lowly differentiated tumors that's why my first thought was ...
written 12 months ago by ciemanek110
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Comment: C: Categorize patients based on continuous variables
... Yes, this was more or less my reasoning: to cluster patients based on all genes in both signatures and then set a cut-off on the branches. Would it be reasonable then to perform transcriptome-wide differential gene expression testing and co-expression analysis between two groups on such classified d ...
written 12 months ago by ciemanek110
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Categorize patients based on continuous variables
... Hi! My problem concerns categorizing patients to groups based on continuous variables. From the previous studies we know that there are continuous differences in mean expression of two signatures, which are negatively correlated. We are interested in comparing two extreme groups in terms of differe ...
biostatictics expression written 12 months ago by ciemanek110 • updated 12 months ago by dariober9.9k
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Comment: C: affy MAplot NA error
... Thanks a lot Kevin! However, if I understand correctly from the vignette you recommended, it should be possible to make an MA plot from AffyBatch object, including object with the raw data - the function should by default transform it to logarithms? All the best, Agata *** EDIT *** I managed to ...
written 14 months ago by ciemanek110
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affy MAplot NA error
... Hi all! I am trying to draw MA plots for my Affymetrix microarrays using affy package and function MAplot. I am trying to take a look at my raw data in AffyBatch object (1st microarray) as follows: MAplot(data.raw, which=1) However, I am keep on gettin an error stating: Error in quantile ...
maplot quantile affy microarrays affymetrix written 14 months ago by ciemanek110 • updated 14 months ago by Kevin Blighe39k

Latest awards to ciemanek

Popular Question 9 months ago, created a question with more than 1,000 views. For bwa aln for paired-end sequencing data in one .fastq file
Popular Question 20 months ago, created a question with more than 1,000 views. For VarScan and Samtools - how to process my data?

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