User: MWSchmid

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MWSchmid0
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Posts by MWSchmid

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Comment: C: Extract residuals from DESeq2 fit
... Though - wouldn't it be possible to use deviances instead of the residuals? ...
written 3 months ago by MWSchmid0
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Comment: C: Extract residuals from DESeq2 fit
... Thanks for your help. I will have a look at the VST data. ...
written 3 months ago by MWSchmid0
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Extract residuals from DESeq2 fit
... Hi there I'm not sure how it's called what I'm trying to do, but I would like to extract (residuals of) normalized expression/abundance values that are "corrected/adjusted" for certain design factors. For example, using the regular lm(), I can correct for spatial variation (characterized by a bunc ...
deseq2 residuals written 3 months ago by MWSchmid0 • updated 3 months ago by Michael Love26k
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Answer: A: Rsubread on Cygwin - error due to gcc ... -D MACOS - why?
... Ok - I tried now to fall back to pthread_spin_XXX instead of pthread_mutex_XXX. I did this with once with erasing #define USE_POSIX_MUTEX_LOCK and another time with #undef USE_POSIX_MUTEX_LOCK just before the if statement for the switch (in subread.h). Assuming that this is enough (is it?), there is ...
written 3.3 years ago by MWSchmid0
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Answer: A: Rsubread on Cygwin - error due to gcc ... -D MACOS - why?
... Thanks for the hint - I will have a look whether I find a solution for this. Searching for pthread mutex and Cygwin looks like there were several issues in the past. I will post an update if I can solve it in some way. ...
written 3.4 years ago by MWSchmid0
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Comment: C: Rsubread on Cygwin - error due to gcc ... -D MACOS - why?
... I tested it now with an uncompressed fastq - and in a second step also with writing SAM instead of BAM. It's the same slow as before and only uses one CPU instead of the specified amount. Any other idea?   ...
written 3.4 years ago by MWSchmid0
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Answer: A: Rsubread on Cygwin - error due to gcc ... -D MACOS - why?
... Tested it briefly - it works, but it's very slow compared to the old version of Rsubread (1.16). It seems not to be able to use several CPUs at once - might be due to on-the-fly decompression (in the past it decompressed the file first and then aligned all the reads) - ? ...
written 3.4 years ago by MWSchmid0
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Answer: A: Rsubread on Cygwin - error due to gcc ... -D MACOS - why?
... Hm - replacing if(feof(input_file.input_fp))break; in build-sam-index.c with if(feof((FILE *)input_file.input_fp))break; brought me now through the compilation. ...
written 3.4 years ago by MWSchmid0
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Answer: A: Rsubread on Cygwin - error due to gcc ... -D MACOS - why?
... Ok - I know why it uses MACOS - the fall-through in "configure" is MacOS:   #!/bin/sh #cp src/Makevars.in src/Makevars UNAME=`uname` echo @@@@@ The operating system is $UNAME. version_no=`cat DESCRIPTION |grep Version|cut -f2 -d' '` echo SUBREAD_VER = \"\\\"Rsubread $version_no\\\"\" > src/Mak ...
written 3.4 years ago by MWSchmid0
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Rsubread on Cygwin - error due to gcc ... -D MACOS - why?
... Hi there I recently tried to install Rsubread on Cygwin. I did that a few months ago successfully and now I tried it with the same steps as last time (I wrote quite detailed instructions last time). Of course, the machine is different - last time I had Win7, R 3.1.3 installed in CYGWIN_NT-6.1 and R ...
rsubread written 3.4 years ago by MWSchmid0 • updated 3.3 years ago by Wei Shi3.2k

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